metadata: run_metadata: 51 rows where devstage_curation = "Juvenile" and technology = "bulk"

51 rows where devstage_curation = "Juvenile" and technology = "bulk"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.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
24588	24588	SRR25462256	SRX21195045	SRS18453971	SRP452270	PRJNA1000445	CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption	GSE239622	Transcriptome Analysis	CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…			PG HE 50dpf 3	GSM7669021	source name:follicle\|strain:AB\|tissue:follicle\|developmental stage:primary growth\|age:50dpf\|genotype:HE cdkn1a +/ \|geo loc name:missing\|collection date:missing	PG HE 50dpf 3	Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file	follicle		TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina		strain:AB\|tissue:follicle\|developmental stage:primary growth\|age:50dpf\|genotype:HE cdkn1a +/	GSM7669021	GSM7669021: PG HE 50dpf 3; Danio rerio; RNA Seq	GSM7669021 r1	GSM7669021	1	TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP452270		PG_HE_3_S26_L003_R1_001.fastq.gz PG_HE_3_S26_L003_R2_001.fastq.gz	fastq fastq	4520051001.0	22984712.0	GSM7669021 r1	0:98.32 1:98.33	A:1134815259;C:1102592573;G:1104475707;T:1160918938;N:17248524	98	98	1134815259	1102592573	1104475707	1160918938	17248524	SRX21195045	SRS18453971			Karp 12006A, Biology of Vascular Program, Boston Children's Hospital	2	0.93438	0.93937	0.01237	0.01252	0.78208	0.78192	0.48454	0.49474	99	99	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	United States	2023-07-31	Juvenile	Juvenile	Gonad	Reproductive System
24589	24589	SRR25462257	SRX21195044	SRS18453970	SRP452270	PRJNA1000445	CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption	GSE239622	Transcriptome Analysis	CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…			PG HE 50dpf 2	GSM7669020	source name:follicle\|strain:AB\|tissue:follicle\|developmental stage:primary growth\|age:50dpf\|genotype:HE cdkn1a +/ \|geo loc name:missing\|collection date:missing	PG HE 50dpf 2	Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file	follicle		TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina		strain:AB\|tissue:follicle\|developmental stage:primary growth\|age:50dpf\|genotype:HE cdkn1a +/	GSM7669020	GSM7669020: PG HE 50dpf 2; Danio rerio; RNA Seq	GSM7669020 r1	GSM7669020	1	TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP452270		PG_HE_2_S25_L003_R2_001.fastq.gz PG_HE_2_S25_L003_R1_001.fastq.gz	fastq fastq	3915471868.0	19847479.0	GSM7669020 r1	0:98.64 1:98.64	A:982714666;C:957212118;G:961590362;T:1003408448;N:10546274	98	98	982714666	957212118	961590362	1003408448	10546274	SRX21195044	SRS18453970			Karp 12006A, Biology of Vascular Program, Boston Children's Hospital	2	0.93184	0.93552	0.01275	0.01275	0.78356	0.7835	0.49472	0.48841	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	United States	2023-07-31	Juvenile	Juvenile	Gonad	Reproductive System
24590	24590	SRR25462258	SRX21195043	SRS18453969	SRP452270	PRJNA1000445	CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption	GSE239622	Transcriptome Analysis	CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…			PG HE 50dpf 1	GSM7669019	source name:follicle\|strain:AB\|tissue:follicle\|developmental stage:primary growth\|age:50dpf\|genotype:HE cdkn1a +/ \|geo loc name:missing\|collection date:missing	PG HE 50dpf 1	Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file	follicle		TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina		strain:AB\|tissue:follicle\|developmental stage:primary growth\|age:50dpf\|genotype:HE cdkn1a +/	GSM7669019	GSM7669019: PG HE 50dpf 1; Danio rerio; RNA Seq	GSM7669019 r1	GSM7669019	1	TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP452270		PG_HE_1_S24_L003_R1_001.fastq.gz PG_HE_1_S24_L003_R2_001.fastq.gz	fastq fastq	4764998144.0	24264412.0	GSM7669019 r1	0:98.18 1:98.20	A:1194676445;C:1161648051;G:1165061360;T:1221860864;N:21751424	98	98	1194676445	1161648051	1165061360	1221860864	21751424	SRX21195043	SRS18453969			Karp 12006A, Biology of Vascular Program, Boston Children's Hospital	2	0.91864	0.92247	0.01213	0.01245	0.7949	0.79584	0.50422	0.50318	100	98	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	United States	2023-07-31	Juvenile	Juvenile	Gonad	Reproductive System
24591	24591	SRR25462259	SRX21195042	SRS18453968	SRP452270	PRJNA1000445	CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption	GSE239622	Transcriptome Analysis	CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…			PG WT 50dpf 3	GSM7669018	source name:follicle\|strain:AB\|tissue:follicle\|developmental stage:primary growth\|age:50dpf\|genotype:WT cdkn1a +/+\|geo loc name:missing\|collection date:missing	PG WT 50dpf 3	Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file	follicle		TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina		strain:AB\|tissue:follicle\|developmental stage:primary growth\|age:50dpf\|genotype:WT cdkn1a +/+	GSM7669018	GSM7669018: PG WT 50dpf 3; Danio rerio; RNA Seq	GSM7669018 r1	GSM7669018	1	TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP452270		PG_WT_3_S23_L003_R1_001.fastq.gz PG_WT_3_S23_L003_R2_001.fastq.gz	fastq fastq	6204452412.0	31480139.0	GSM7669018 r1	0:98.55 1:98.54	A:1567898375;C:1505755791;G:1512895523;T:1599284546;N:18618177	98	98	1567898375	1505755791	1512895523	1599284546	18618177	SRX21195042	SRS18453968			Karp 12006A, Biology of Vascular Program, Boston Children's Hospital	2	0.9312	0.93599	0.01692	0.01686	0.76426	0.76439	0.46519	0.47751	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	United States	2023-07-31	Juvenile	Juvenile	Gonad	Reproductive System
24592	24592	SRR25462260	SRX21195041	SRS18453967	SRP452270	PRJNA1000445	CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption	GSE239622	Transcriptome Analysis	CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…			PG WT 50dpf 2	GSM7669017	source name:follicle\|strain:AB\|tissue:follicle\|developmental stage:primary growth\|age:50dpf\|genotype:WT cdkn1a +/+\|geo loc name:missing\|collection date:missing	PG WT 50dpf 2	Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file	follicle		TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina		strain:AB\|tissue:follicle\|developmental stage:primary growth\|age:50dpf\|genotype:WT cdkn1a +/+	GSM7669017	GSM7669017: PG WT 50dpf 2; Danio rerio; RNA Seq	GSM7669017 r1	GSM7669017	1	TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP452270		PG_WT_2_S22_L003_R1_001.fastq.gz PG_WT_2_S22_L003_R2_001.fastq.gz	fastq fastq	3907759829.0	19906505.0	GSM7669017 r1	0:98.15 1:98.15	A:991973983;C:940499355;G:946342572;T:1011476708;N:17467211	98	98	991973983	940499355	946342572	1011476708	17467211	SRX21195041	SRS18453967			Karp 12006A, Biology of Vascular Program, Boston Children's Hospital	2	0.91435	0.9186	0.02035	0.02032	0.764	0.76321	0.48743	0.48644	97	99	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	United States	2023-07-31	Juvenile	Juvenile	Gonad	Reproductive System
24593	24593	SRR25462261	SRX21195040	SRS18453966	SRP452270	PRJNA1000445	CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption	GSE239622	Transcriptome Analysis	CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…			PG WT 50dpf 1	GSM7669016	source name:follicle\|strain:AB\|tissue:follicle\|developmental stage:primary growth\|age:50dpf\|genotype:WT cdkn1a +/+\|geo loc name:missing\|collection date:missing	PG WT 50dpf 1	Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file	follicle		TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina		strain:AB\|tissue:follicle\|developmental stage:primary growth\|age:50dpf\|genotype:WT cdkn1a +/+	GSM7669016	GSM7669016: PG WT 50dpf 1; Danio rerio; RNA Seq	GSM7669016 r1	GSM7669016	1	TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP452270		PG_WT_1_S21_L003_R2_001.fastq.gz PG_WT_1_S21_L003_R1_001.fastq.gz	fastq fastq	7395136401.0	37752582.0	GSM7669016 r1	0:97.94 1:97.94	A:1865709287;C:1789949400;G:1796311820;T:1908470411;N:34695483	97	97	1865709287	1789949400	1796311820	1908470411	34695483	SRX21195040	SRS18453966			Karp 12006A, Biology of Vascular Program, Boston Children's Hospital	2	0.9216	0.92737	0.01817	0.01802	0.76601	0.76593	0.48894	0.4975	100	99	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	United States	2023-07-31	Juvenile	Juvenile	Gonad	Reproductive System
26487	26487	SRR26034371	SRX21751586	SRS18859093	SRP459779	PRJNA1015242	Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.	GSE242897	Transcriptome Analysis	Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals 3 individual tp53 mutant and ptch1 crispant animals and 3 individual tp53 heterozygous and ptch1 crispant animals.		pubmed:39078737	19521X6 tp53het tumor	GSM7774462	source name:brain\|tissue:brain\|tumor status:tumor\|age:7 wpf\|genotype:tp53 heterozygous\|geo loc name:missing\|collection date:missing	19521X6 tp53het tumor	The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts.	brain	Brains were frozen at 80C in RNA stabilization solution QIAGEN.	Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.	Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.	tissue:brain\|tumor status:tumor\|age:7 wpf\|genotype:tp53 heterozygous	GSM7774462	GSM7774462: 19521X6 tp53het tumor; Danio rerio; RNA Seq	GSM7774462 r1	GSM7774462	1	Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP459779	loader:fastq load.py	19521X6_220211_A00421_0418_AHGVTMDSX3_S177_L003_R1_001.fastq.gz 19521X6_220211_A00421_0418_AHGVTMDSX3_S177_L003_R2_001.fastq.gz	fastq fastq	13856710696.0	45883148.0	GSM7774462 r1	0:151 1:151	A:3910050404;C:3019565763;G:3183961340;T:3742992264;N:140925	151	151	3910050404	3019565763	3183961340	3742992264	140925	SRX21751586	SRS18859093	SRA1710210	Huntsman Cancer Institute	Oncological Sciences, University of Utah	2	0.8794	0.87909	0.38495	0.38479	0.69753	0.70005	0.49322	0.49442	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	rrna_depletion	trueseq	bulk	bulk	bulk	United States	2023-09-11	Juvenile	Juvenile	Brain	Nervous System
26488	26488	SRR26034372	SRX21751585	SRS18859092	SRP459779	PRJNA1015242	Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.	GSE242897	Transcriptome Analysis	Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals 3 individual tp53 mutant and ptch1 crispant animals and 3 individual tp53 heterozygous and ptch1 crispant animals.		pubmed:39078737	19521X5 tp53het tumor	GSM7774461	source name:brain\|tissue:brain\|tumor status:tumor\|age:7 wpf\|genotype:tp53 heterozygous\|geo loc name:missing\|collection date:missing	19521X5 tp53het tumor	The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts.	brain	Brains were frozen at 80C in RNA stabilization solution QIAGEN.	Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.	Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.	tissue:brain\|tumor status:tumor\|age:7 wpf\|genotype:tp53 heterozygous	GSM7774461	GSM7774461: 19521X5 tp53het tumor; Danio rerio; RNA Seq	GSM7774461 r1	GSM7774461	1	Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP459779	loader:fastq load.py	19521X5_220211_A00421_0418_AHGVTMDSX3_S176_L003_R1_001.fastq.gz 19521X5_220211_A00421_0418_AHGVTMDSX3_S176_L003_R2_001.fastq.gz	fastq fastq	18644081740.0	61735370.0	GSM7774461 r1	0:151 1:151	A:5198614433;C:4108657498;G:4307546758;T:5029072002;N:191049	151	151	5198614433	4108657498	4307546758	5029072002	191049	SRX21751585	SRS18859092	SRA1710210	Huntsman Cancer Institute	Oncological Sciences, University of Utah	2	0.88544	0.88842	0.35896	0.35863	0.69193	0.69248	0.49682	0.50274	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	rrna_depletion	trueseq	bulk	bulk	bulk	United States	2023-09-11	Juvenile	Juvenile	Brain	Nervous System
26489	26489	SRR26034373	SRX21751584	SRS18859091	SRP459779	PRJNA1015242	Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.	GSE242897	Transcriptome Analysis	Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals 3 individual tp53 mutant and ptch1 crispant animals and 3 individual tp53 heterozygous and ptch1 crispant animals.		pubmed:39078737	19521X4 tp53het tumor	GSM7774460	source name:brain\|tissue:brain\|tumor status:tumor\|age:7 wpf\|genotype:tp53 heterozygous\|geo loc name:missing\|collection date:missing	19521X4 tp53het tumor	The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts.	brain	Brains were frozen at 80C in RNA stabilization solution QIAGEN.	Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.	Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.	tissue:brain\|tumor status:tumor\|age:7 wpf\|genotype:tp53 heterozygous	GSM7774460	GSM7774460: 19521X4 tp53het tumor; Danio rerio; RNA Seq	GSM7774460 r1	GSM7774460	1	Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP459779	loader:fastq load.py	19521X4_220211_A00421_0418_AHGVTMDSX3_S175_L003_R1_001.fastq.gz 19521X4_220211_A00421_0418_AHGVTMDSX3_S175_L003_R2_001.fastq.gz	fastq fastq	14417628886.0	47740493.0	GSM7774460 r1	0:151 1:151	A:4016299076;C:3183962020;G:3341158152;T:3876059438;N:150200	151	151	4016299076	3183962020	3341158152	3876059438	150200	SRX21751584	SRS18859091	SRA1710210	Huntsman Cancer Institute	Oncological Sciences, University of Utah	2	0.89118	0.89184	0.33812	0.33641	0.68947	0.68954	0.49867	0.50026	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	rrna_depletion	trueseq	bulk	bulk	bulk	United States	2023-09-11	Juvenile	Juvenile	Brain	Nervous System
26491	26491	SRR26034375	SRX21751582	SRS18859089	SRP459779	PRJNA1015242	Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.	GSE242897	Transcriptome Analysis	Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals 3 individual tp53 mutant and ptch1 crispant animals and 3 individual tp53 heterozygous and ptch1 crispant animals.		pubmed:39078737	19521X2 tp53mut tumor	GSM7774458	source name:brain\|tissue:brain\|tumor status:tumor\|age:8 wpf\|genotype:tp53 mutant\|geo loc name:missing\|collection date:missing	19521X2 tp53mut tumor	The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts.	brain	Brains were frozen at 80C in RNA stabilization solution QIAGEN.	Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.	Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.	tissue:brain\|tumor status:tumor\|age:8 wpf\|genotype:tp53 mutant	GSM7774458	GSM7774458: 19521X2 tp53mut tumor; Danio rerio; RNA Seq	GSM7774458 r1	GSM7774458	1	Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP459779	loader:fastq load.py	19521X2_220211_A00421_0418_AHGVTMDSX3_S173_L003_R1_001.fastq.gz 19521X2_220211_A00421_0418_AHGVTMDSX3_S173_L003_R2_001.fastq.gz	fastq fastq	14064076580.0	46569790.0	GSM7774458 r1	0:151 1:151	A:3935649548;C:3089754695;G:3257286821;T:3781242542;N:142974	151	151	3935649548	3089754695	3257286821	3781242542	142974	SRX21751582	SRS18859089	SRA1710210	Huntsman Cancer Institute	Oncological Sciences, University of Utah	2	0.89595	0.89655	0.35454	0.35431	0.68927	0.69077	0.47888	0.47831	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	rrna_depletion	trueseq	bulk	bulk	bulk	United States	2023-09-11	Juvenile	Juvenile	Brain	Nervous System
26492	26492	SRR26034376	SRX21751581	SRS18859088	SRP459779	PRJNA1015242	Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.	GSE242897	Transcriptome Analysis	Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals 3 individual tp53 mutant and ptch1 crispant animals and 3 individual tp53 heterozygous and ptch1 crispant animals.		pubmed:39078737	19521X1 tp53mut tumor	GSM7774457	source name:brain\|tissue:brain\|tumor status:tumor\|age:7 wpf\|genotype:tp53 mutant\|geo loc name:missing\|collection date:missing	19521X1 tp53mut tumor	The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id log2FC padj and raw counts.	brain	Brains were frozen at 80C in RNA stabilization solution QIAGEN.	Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.	Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.	tissue:brain\|tumor status:tumor\|age:7 wpf\|genotype:tp53 mutant	GSM7774457	GSM7774457: 19521X1 tp53mut tumor; Danio rerio; RNA Seq	GSM7774457 r1	GSM7774457	1	Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP459779	loader:fastq load.py	19521X1_220211_A00421_0418_AHGVTMDSX3_S172_L003_R1_001.fastq.gz 19521X1_220211_A00421_0418_AHGVTMDSX3_S172_L003_R2_001.fastq.gz	fastq fastq	16911500190.0	55998345.0	GSM7774457 r1	0:151 1:151	A:4750241986;C:3698380612;G:3890633834;T:4572071732;N:172026	151	151	4750241986	3698380612	3890633834	4572071732	172026	SRX21751581	SRS18859088	SRA1710210	Huntsman Cancer Institute	Oncological Sciences, University of Utah	2	0.89695	0.89831	0.3562	0.35542	0.68392	0.68369	0.48172	0.48641	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	rrna_depletion	trueseq	bulk	bulk	bulk	United States	2023-09-11	Juvenile	Juvenile	Brain	Nervous System
53495	53495	SRR9886611	SRX6639067	SRS5209782	SRP217245	PRJNA558074	Transcriptomic analysis of dj 1 / zebrafish brains compared to wild type siblings	GSE135271	Transcriptome Analysis	RNA Seq comparing transcript expression in the brains of 3 dj 1 / mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1 / zebrafish were generated by deep sequencing in triplicate using Illumina HiSeq 3000		pubmed:32859696	GH6	GSM4002525	source name:Brain\|strain:LWT\|tissue:Brain\|age:12 wpf dj 1 /	GH6	A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript hypertext markup language document including read counts per sample	Brain		Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.		strain:LWT\|tissue:Brain\|age:12 wpf dj 1 /	GSM4002525	GSM4002525: GH6; Danio rerio; RNA Seq	GSM4002525		1	Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.	GEO Accession:GSM4002525	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP217245		GH6_S41_L004_R1_001.fastq-004.gz GH6_S41_L004_R2_001.fastq-009.gz	fastq fastq	16197223984.0	53633192.0	GSM4002525 r1	0:151 1:151	A:4524520245;C:3580881754;G:3728671047;T:4362276906;N:874032	151	151	4524520245	3580881754	3728671047	4362276906	874032	SRX6639067	SRS5209782	SRA931013	GEO	Biology, University of York	2	0.91745	0.9163	0.15171	0.14974	0.69826	0.70161	0.49509	0.48979	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	United Kingdom	2019-08-01	Juvenile	Juvenile	Brain	Nervous System
53496	53496	SRR9886610	SRX6639066	SRS5209781	SRP217245	PRJNA558074	Transcriptomic analysis of dj 1 / zebrafish brains compared to wild type siblings	GSE135271	Transcriptome Analysis	RNA Seq comparing transcript expression in the brains of 3 dj 1 / mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1 / zebrafish were generated by deep sequencing in triplicate using Illumina HiSeq 3000		pubmed:32859696	GH5	GSM4002524	source name:Brain\|strain:LWT\|tissue:Brain\|age:12 wpf dj 1 /	GH5	A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript hypertext markup language document including read counts per sample	Brain		Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.		strain:LWT\|tissue:Brain\|age:12 wpf dj 1 /	GSM4002524	GSM4002524: GH5; Danio rerio; RNA Seq	GSM4002524		1	Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.	GEO Accession:GSM4002524	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP217245		GH5_S40_L004_R1_001.fastq-001.gz GH5_S40_L004_R2_001.fastq-003.gz	fastq fastq	14762621304.0	48882852.0	GSM4002524 r1	0:151 1:151	A:4134788753;C:3245817056;G:3388258601;T:3992937107;N:819787	151	151	4134788753	3245817056	3388258601	3992937107	819787	SRX6639066	SRS5209781	SRA931013	GEO	Biology, University of York	2	0.91356	0.91354	0.15637	0.15448	0.69755	0.70177	0.48873	0.49642	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	United Kingdom	2019-08-01	Juvenile	Juvenile	Brain	Nervous System
53497	53497	SRR9886609	SRX6639065	SRS5209780	SRP217245	PRJNA558074	Transcriptomic analysis of dj 1 / zebrafish brains compared to wild type siblings	GSE135271	Transcriptome Analysis	RNA Seq comparing transcript expression in the brains of 3 dj 1 / mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1 / zebrafish were generated by deep sequencing in triplicate using Illumina HiSeq 3000		pubmed:32859696	GH4	GSM4002523	source name:Brain\|strain:LWT\|tissue:Brain\|age:12 wpf dj 1 /	GH4	A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript hypertext markup language document including read counts per sample	Brain		Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.		strain:LWT\|tissue:Brain\|age:12 wpf dj 1 /	GSM4002523	GSM4002523: GH4; Danio rerio; RNA Seq	GSM4002523		1	Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.	GEO Accession:GSM4002523	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP217245		GH4_S39_L004_R1_001.fastq-008.gz GH4_S39_L004_R2_001.fastq-011.gz	fastq fastq	17232418376.0	57060988.0	GSM4002523 r1	0:151 1:151	A:4798343141;C:3812370940;G:3947002545;T:4673748329;N:953421	151	151	4798343141	3812370940	3947002545	4673748329	953421	SRX6639065	SRS5209780	SRA931013	GEO	Biology, University of York	2	0.91359	0.91289	0.15791	0.15599	0.70128	0.70585	0.48423	0.48897	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	United Kingdom	2019-08-01	Juvenile	Juvenile	Brain	Nervous System
53498	53498	SRR9886608	SRX6639064	SRS5209779	SRP217245	PRJNA558074	Transcriptomic analysis of dj 1 / zebrafish brains compared to wild type siblings	GSE135271	Transcriptome Analysis	RNA Seq comparing transcript expression in the brains of 3 dj 1 / mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1 / zebrafish were generated by deep sequencing in triplicate using Illumina HiSeq 3000		pubmed:32859696	GH3	GSM4002522	source name:Brain\|strain:LWT\|tissue:Brain\|age:12 wpf type	GH3	A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript hypertext markup language document including read counts per sample	Brain		Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.		strain:LWT\|tissue:Brain\|age:12 wpf type	GSM4002522	GSM4002522: GH3; Danio rerio; RNA Seq	GSM4002522		1	Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.	GEO Accession:GSM4002522	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP217245		GH3_S38_L004_R1_001.fastq-002.gz GH3_S38_L004_R2_001.fastq-005.gz	fastq fastq	15880659430.0	52584965.0	GSM4002522 r1	0:151 1:151	A:4428460730;C:3500855291;G:3647161094;T:4303300463;N:881852	151	151	4428460730	3500855291	3647161094	4303300463	881852	SRX6639064	SRS5209779	SRA931013	GEO	Biology, University of York	2	0.91311	0.91404	0.15734	0.15592	0.69621	0.70092	0.4936	0.48217	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	United Kingdom	2019-08-01	Juvenile	Juvenile	Brain	Nervous System
53499	53499	SRR9886607	SRX6639063	SRS5209778	SRP217245	PRJNA558074	Transcriptomic analysis of dj 1 / zebrafish brains compared to wild type siblings	GSE135271	Transcriptome Analysis	RNA Seq comparing transcript expression in the brains of 3 dj 1 / mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1 / zebrafish were generated by deep sequencing in triplicate using Illumina HiSeq 3000		pubmed:32859696	GH2	GSM4002521	source name:Brain\|strain:LWT\|tissue:Brain\|age:12 wpf type	GH2	A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript hypertext markup language document including read counts per sample	Brain		Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.		strain:LWT\|tissue:Brain\|age:12 wpf type	GSM4002521	GSM4002521: GH2; Danio rerio; RNA Seq	GSM4002521		1	Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.	GEO Accession:GSM4002521	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP217245		GH2_S37_L004_R1_001.fastq-006.gz GH2_S37_L004_R2_001.fastq-012.gz	fastq fastq	17721573816.0	58680708.0	GSM4002521 r1	0:151 1:151	A:4948184152;C:3901958410;G:4066182263;T:4804260891;N:988100	151	151	4948184152	3901958410	4066182263	4804260891	988100	SRX6639063	SRS5209778	SRA931013	GEO	Biology, University of York	2	0.90975	0.90966	0.16242	0.16044	0.69934	0.70339	0.48497	0.49335	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	United Kingdom	2019-08-01	Juvenile	Juvenile	Brain	Nervous System
53500	53500	SRR9886606	SRX6639062	SRS5209777	SRP217245	PRJNA558074	Transcriptomic analysis of dj 1 / zebrafish brains compared to wild type siblings	GSE135271	Transcriptome Analysis	RNA Seq comparing transcript expression in the brains of 3 dj 1 / mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1 / zebrafish were generated by deep sequencing in triplicate using Illumina HiSeq 3000		pubmed:32859696	GH1	GSM4002520	source name:Brain\|strain:LWT\|tissue:Brain\|age:12 wpf type	GH1	A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript hypertext markup language document including read counts per sample	Brain		Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.		strain:LWT\|tissue:Brain\|age:12 wpf type	GSM4002520	GSM4002520: GH1; Danio rerio; RNA Seq	GSM4002520		1	Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions.	GEO Accession:GSM4002520	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP217245		GH1_S36_L004_R1_001.fastq-007.gz GH1_S36_L004_R2_001.fastq-010.gz	fastq fastq	16852076254.0	55801577.0	GSM4002520 r1	0:151 1:151	A:4697089825;C:3744087924;G:3878965083;T:4531030410;N:903012	151	151	4697089825	3744087924	3878965083	4531030410	903012	SRX6639062	SRS5209777	SRA931013	GEO	Biology, University of York	2	0.91719	0.91765	0.15136	0.15011	0.69998	0.70455	0.48284	0.48335	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	United Kingdom	2019-08-01	Juvenile	Juvenile	Brain	Nervous System
60916	60916	SRR12658664	SRX9139722	SRS7381388	SRP282671	PRJNA663959	Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development	GSE158098	Transcriptome Analysis	Here we used RNA sequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNA seq was performed on surgically dissected kidneys from wild type and runx1 / siblings 2.5 mpf pool of 3 kidneys/replicate n= 3 for each genotype.	parent bioproject:PRJNA663961	pubmed:34492681	runx1 / kidney3	GSM4792207	source name:adult kidney\|strain:EK\|genotype/variation:runx1 / del25 hg97\|age:2.5 month\|tissue:kidney	runx1 / kidney3	RNA seq reads were aligned to the zebrafish genome reference GRCz10 and transcript reference GRCz10.87 using STAR v2.5.26. We used RSEM to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz10 Supplementary files format and content: *.count.txt: Gene expression count matrix.	adult kidney		RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in 80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.		strain:EK\|genotype/variation:runx1 / del25 hg97\|age:2.5 month\|tissue:kidney	GSM4792207	GSM4792207: runx1 / kidney3; Danio rerio; RNA Seq	GSM4792207		1	RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in 80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.	GEO Accession:GSM4792207	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP282671		runx1_del25_null_6.1.cln.fq.gz runx1_del25_null_6.2.cln.fq.gz	fastq fastq	9833070492.0	39020121.0	GSM4792207 r1	0:126 1:126	A:2595482323;C:2237794410;G:2283114442;T:2716679317;N:0	126	126	2595482323	2237794410	2283114442	2716679317	0	SRX9139722	SRS7381388	SRA1126725	GEO	NHGRI	2	0.95072	0.95176	0.08254	0.08278	0.72565	0.7265	0.55513	0.55433	126	126	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2020-09-16	Juvenile	Juvenile	Kidney	Renal System
60917	60917	SRR12658663	SRX9139721	SRS7381387	SRP282671	PRJNA663959	Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development	GSE158098	Transcriptome Analysis	Here we used RNA sequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNA seq was performed on surgically dissected kidneys from wild type and runx1 / siblings 2.5 mpf pool of 3 kidneys/replicate n= 3 for each genotype.	parent bioproject:PRJNA663961	pubmed:34492681	runx1 / kidney2	GSM4792206	source name:adult kidney\|strain:EK\|genotype/variation:runx1 / del25 hg97\|age:2.5 month\|tissue:kidney	runx1 / kidney2	RNA seq reads were aligned to the zebrafish genome reference GRCz10 and transcript reference GRCz10.87 using STAR v2.5.26. We used RSEM to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz10 Supplementary files format and content: *.count.txt: Gene expression count matrix.	adult kidney		RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in 80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.		strain:EK\|genotype/variation:runx1 / del25 hg97\|age:2.5 month\|tissue:kidney	GSM4792206	GSM4792206: runx1 / kidney2; Danio rerio; RNA Seq	GSM4792206		1	RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in 80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.	GEO Accession:GSM4792206	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP282671		runx1_del25_null_5.1.cln.fq.gz runx1_del25_null_5.2.cln.fq.gz	fastq fastq	10411105572.0	41313911.0	GSM4792206 r1	0:126 1:126	A:2758731492;C:2362241256;G:2412281429;T:2877851395;N:0	126	126	2758731492	2362241256	2412281429	2877851395	0	SRX9139721	SRS7381387	SRA1126725	GEO	NHGRI	2	0.9462	0.94718	0.09575	0.09572	0.74282	0.74391	0.53729	0.53866	126	126	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2020-09-16	Juvenile	Juvenile	Kidney	Renal System
60918	60918	SRR12658662	SRX9139720	SRS7381386	SRP282671	PRJNA663959	Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development	GSE158098	Transcriptome Analysis	Here we used RNA sequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNA seq was performed on surgically dissected kidneys from wild type and runx1 / siblings 2.5 mpf pool of 3 kidneys/replicate n= 3 for each genotype.	parent bioproject:PRJNA663961	pubmed:34492681	runx1 / kidney1	GSM4792205	source name:adult kidney\|strain:EK\|genotype/variation:runx1 / del25 hg97\|age:2.5 month\|tissue:kidney	runx1 / kidney1	RNA seq reads were aligned to the zebrafish genome reference GRCz10 and transcript reference GRCz10.87 using STAR v2.5.26. We used RSEM to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz10 Supplementary files format and content: *.count.txt: Gene expression count matrix.	adult kidney		RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in 80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.		strain:EK\|genotype/variation:runx1 / del25 hg97\|age:2.5 month\|tissue:kidney	GSM4792205	GSM4792205: runx1 / kidney1; Danio rerio; RNA Seq	GSM4792205		1	RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in 80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.	GEO Accession:GSM4792205	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP282671		runx1_del25_null_4.1.cln.fq.gz runx1_del25_null_4.2.cln.fq.gz	fastq fastq	6973886556.0	27674153.0	GSM4792205 r1	0:126 1:126	A:1932833306;C:1502732434;G:1534451974;T:2003868842;N:0	126	126	1932833306	1502732434	1534451974	2003868842	0	SRX9139720	SRS7381386	SRA1126725	GEO	NHGRI	2	0.93692	0.93786	0.11567	0.11588	0.74123	0.74099	0.56167	0.56297	126	126	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2020-09-16	Juvenile	Juvenile	Kidney	Renal System
60919	60919	SRR12658661	SRX9139719	SRS7381385	SRP282671	PRJNA663959	Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development	GSE158098	Transcriptome Analysis	Here we used RNA sequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNA seq was performed on surgically dissected kidneys from wild type and runx1 / siblings 2.5 mpf pool of 3 kidneys/replicate n= 3 for each genotype.	parent bioproject:PRJNA663961	pubmed:34492681	WT kidney3	GSM4792204	source name:adult kidney\|strain:EK\|genotype/variation:WT\|age:2.5 month\|tissue:kidney	WT kidney3	RNA seq reads were aligned to the zebrafish genome reference GRCz10 and transcript reference GRCz10.87 using STAR v2.5.26. We used RSEM to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz10 Supplementary files format and content: *.count.txt: Gene expression count matrix.	adult kidney		RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in 80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.		strain:EK\|genotype/variation:WT\|age:2.5 month\|tissue:kidney	GSM4792204	GSM4792204: WT kidney3; Danio rerio; RNA Seq	GSM4792204		1	RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in 80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.	GEO Accession:GSM4792204	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP282671		runx1_del25_WT_3.1.cln.fq.gz runx1_del25_WT_3.2.cln.fq.gz	fastq fastq	11183311944.0	44378222.0	GSM4792204 r1	0:126 1:126	A:2920698001;C:2577574528;G:2637485861;T:3047553554;N:0	126	126	2920698001	2577574528	2637485861	3047553554	0	SRX9139719	SRS7381385	SRA1126725	GEO	NHGRI	2	0.95338	0.95426	0.07656	0.07667	0.72693	0.72782	0.51199	0.51082	126	126	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2020-09-16	Juvenile	Juvenile	Kidney	Renal System
60920	60920	SRR12658660	SRX9139718	SRS7381384	SRP282671	PRJNA663959	Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development	GSE158098	Transcriptome Analysis	Here we used RNA sequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNA seq was performed on surgically dissected kidneys from wild type and runx1 / siblings 2.5 mpf pool of 3 kidneys/replicate n= 3 for each genotype.	parent bioproject:PRJNA663961	pubmed:34492681	WT kidney2	GSM4792203	source name:adult kidney\|strain:EK\|genotype/variation:WT\|age:2.5 month\|tissue:kidney	WT kidney2	RNA seq reads were aligned to the zebrafish genome reference GRCz10 and transcript reference GRCz10.87 using STAR v2.5.26. We used RSEM to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz10 Supplementary files format and content: *.count.txt: Gene expression count matrix.	adult kidney		RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in 80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.		strain:EK\|genotype/variation:WT\|age:2.5 month\|tissue:kidney	GSM4792203	GSM4792203: WT kidney2; Danio rerio; RNA Seq	GSM4792203		1	RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in 80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.	GEO Accession:GSM4792203	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP282671		runx1_del25_WT_2.1.cln.fq.gz runx1_del25_WT_2.2.cln.fq.gz	fastq fastq	9052361388.0	35922069.0	GSM4792203 r1	0:126 1:126	A:2412816184;C:2041456610;G:2086024563;T:2512064031;N:0	126	126	2412816184	2041456610	2086024563	2512064031	0	SRX9139718	SRS7381384	SRA1126725	GEO	NHGRI	2	0.94726	0.94854	0.09295	0.09312	0.73198	0.73206	0.54429	0.54313	126	126	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2020-09-16	Juvenile	Juvenile	Kidney	Renal System
60921	60921	SRR12658659	SRX9139717	SRS7381383	SRP282671	PRJNA663959	Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development	GSE158098	Transcriptome Analysis	Here we used RNA sequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNA seq was performed on surgically dissected kidneys from wild type and runx1 / siblings 2.5 mpf pool of 3 kidneys/replicate n= 3 for each genotype.	parent bioproject:PRJNA663961	pubmed:34492681	WT kidney1	GSM4792202	source name:adult kidney\|strain:EK\|genotype/variation:WT\|age:2.5 month\|tissue:kidney	WT kidney1	RNA seq reads were aligned to the zebrafish genome reference GRCz10 and transcript reference GRCz10.87 using STAR v2.5.26. We used RSEM to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz10 Supplementary files format and content: *.count.txt: Gene expression count matrix.	adult kidney		RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in 80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.		strain:EK\|genotype/variation:WT\|age:2.5 month\|tissue:kidney	GSM4792202	GSM4792202: WT kidney1; Danio rerio; RNA Seq	GSM4792202		1	RNA seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from 2.5 mpf fish n= 3 for each genotype pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52oC for 10 min and then overnight in 80oC. RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepared using paired end library preparation TruSeq RNA Library Prep Kit v2.	GEO Accession:GSM4792202	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP282671		runx1_del25_WT_1.1.cln.fq.gz runx1_del25_WT_1.2.cln.fq.gz	fastq fastq	10029561192.0	39799846.0	GSM4792202 r1	0:126 1:126	A:2618335131;C:2316817389;G:2358350895;T:2736057777;N:0	126	126	2618335131	2316817389	2358350895	2736057777	0	SRX9139717	SRS7381383	SRA1126725	GEO	NHGRI	2	0.95028	0.95138	0.08999	0.09004	0.77956	0.78102	0.54427	0.5347	126	126	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2020-09-16	Juvenile	Juvenile	Kidney	Renal System
61643	61643	SRR12899696	SRX9364743	SRS7586958	SRP288615	PRJNA672100	Nrl dependent and independent rod photoreceptor development in zebrafish [RNA Seq]	GSE160138	Transcriptome Analysis	NRL Neural retina leucine zipper is a key regulator of the fate determination and gene expression of rod photoreceptors in the retina of many vertebrates. In this study we observed a unique retinal phenotype in the nrl knockout zebrafish model characterized by reduced rods with shortened outer segments and gradually increased green cones in maturity. By tracing and comparing the developmental processes of WT and nrl knockout rods we found there might be two waves of rod genesis distinguished as nrl dependent and independent with different starting times. To reveal the underlying cellular and molecular mechanisms bulk and single cell RNA seq were performed. The changes in gene expression and cell proportion of rods and cones agreed well with our histological and immunofluorescence studies. Interestingly we found that rods exhibited noticeable heterogeneities in the gene expression patterns and a part of rods in nrl knockout zebrafish misexpressed the green cone genes reflecting a hybrid status of rod and green cone. Furthermore we identified mafba as a novel regulator of rod genesis which was responsible for the development of rods in nrl knockout zebrafish. Our study will largely improve the current understanding of the developmental processes and regulatory mechanisms of rods in zebrafish and probably other species and may facilitate future studies in the fields of retinal development and retinal degeneration. Overall design: Two WT and two nrl KO samples two biological replicates were analyzed. Each sample represented a pool of RNAs from three zebrafish retinas at the age of 2 month. The differentially expressed genes between WT and nrl KO groups were identified.	parent bioproject:PRJNA672094	pubmed:35245286	nrl R2	GSM4861209	source name:Retina\|tissue:Retina\|strain:AB\|age:2 mpf KO	nrl R2	Quality control mapping and expression analysis: Image analysis and base calling were conducted by the HiSeq Control Software HCS + OLB + GAPipeline 1.6 Illumina on the HiSeq instrument. The high quality clean data were generated by Trimmomatic v0.30 and aligned to the reference genome of zebrafish via software Hisat2 v2.0.1. Differential expression analysis: Gene and isoform expression levels were estimated by HTSeq v0.6.1. Differential expression analysis was performed by DESeq Bioconductor package. post adjusted by Benjamini and Hochberg’s approach for controlling the false discovery rate the threshold of p values was set to <0.05 to detect differentially expressed genes. GO and KEGG enrichment analysis: GO TermFinder was used identifying Gene Ontology GO terms that annotate a list of enriched genes with a significant p value less than 0.05. KEGG Kyoto Encyclopedia of Genes and Genomes is a collection of databases dealing with genomes biological pathways diseases drugs and chemical substances http://en.wikipedia.org/wiki/KEGG which was used to enrich significant differential expression gene in KEGG pathways. Genome build: GRCz11 from Ensembl Supplementary files format and content: Tab delimited text files including the raw counts and FPKM values for each Sample Supplementary files format and content: Tab delimited text files showing the foldchanges and p values of the differentially expressed genes	Retina		For each RNA sample three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN ≥9.5 and A260/280 ≥1.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer’s protocol.		tissue:Retina\|strain:AB\|age:2 mpf KO	GSM4861209	GSM4861209: nrl R2; Danio rerio; RNA Seq	GSM4861209		1	For each RNA sample three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN ≥9.5 and A260/280 ≥1.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer's protocol.	GEO Accession:GSM4861209	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP288615		nrl-R2_combined_R1.fastq.gz nrl-R2_combined_R2.fastq.gz	fastq fastq	7231497600.0	24104992.0	GSM4861209 r1	0:150 1:150	A:1995457626;C:1613822880;G:1630032692;T:1991951852;N:232550	150	150	1995457626	1613822880	1630032692	1991951852	232550	SRX9364743	SRS7586958	SRA1147909	GEO	College of Life Science and Technology, Huazhong University of Science and Technology	2	0.91539	0.91383	0.13441	0.13499	0.69296	0.70021	0.5139	0.50426	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc_generic	bulk	bulk	China	2020-10-26	Juvenile	Juvenile	Eye	Sensory System
61644	61644	SRR12899695	SRX9364742	SRS7586957	SRP288615	PRJNA672100	Nrl dependent and independent rod photoreceptor development in zebrafish [RNA Seq]	GSE160138	Transcriptome Analysis	NRL Neural retina leucine zipper is a key regulator of the fate determination and gene expression of rod photoreceptors in the retina of many vertebrates. In this study we observed a unique retinal phenotype in the nrl knockout zebrafish model characterized by reduced rods with shortened outer segments and gradually increased green cones in maturity. By tracing and comparing the developmental processes of WT and nrl knockout rods we found there might be two waves of rod genesis distinguished as nrl dependent and independent with different starting times. To reveal the underlying cellular and molecular mechanisms bulk and single cell RNA seq were performed. The changes in gene expression and cell proportion of rods and cones agreed well with our histological and immunofluorescence studies. Interestingly we found that rods exhibited noticeable heterogeneities in the gene expression patterns and a part of rods in nrl knockout zebrafish misexpressed the green cone genes reflecting a hybrid status of rod and green cone. Furthermore we identified mafba as a novel regulator of rod genesis which was responsible for the development of rods in nrl knockout zebrafish. Our study will largely improve the current understanding of the developmental processes and regulatory mechanisms of rods in zebrafish and probably other species and may facilitate future studies in the fields of retinal development and retinal degeneration. Overall design: Two WT and two nrl KO samples two biological replicates were analyzed. Each sample represented a pool of RNAs from three zebrafish retinas at the age of 2 month. The differentially expressed genes between WT and nrl KO groups were identified.	parent bioproject:PRJNA672094	pubmed:35245286	nrl R1	GSM4861208	source name:Retina\|tissue:Retina\|strain:AB\|age:2 mpf KO	nrl R1	Quality control mapping and expression analysis: Image analysis and base calling were conducted by the HiSeq Control Software HCS + OLB + GAPipeline 1.6 Illumina on the HiSeq instrument. The high quality clean data were generated by Trimmomatic v0.30 and aligned to the reference genome of zebrafish via software Hisat2 v2.0.1. Differential expression analysis: Gene and isoform expression levels were estimated by HTSeq v0.6.1. Differential expression analysis was performed by DESeq Bioconductor package. post adjusted by Benjamini and Hochberg’s approach for controlling the false discovery rate the threshold of p values was set to <0.05 to detect differentially expressed genes. GO and KEGG enrichment analysis: GO TermFinder was used identifying Gene Ontology GO terms that annotate a list of enriched genes with a significant p value less than 0.05. KEGG Kyoto Encyclopedia of Genes and Genomes is a collection of databases dealing with genomes biological pathways diseases drugs and chemical substances http://en.wikipedia.org/wiki/KEGG which was used to enrich significant differential expression gene in KEGG pathways. Genome build: GRCz11 from Ensembl Supplementary files format and content: Tab delimited text files including the raw counts and FPKM values for each Sample Supplementary files format and content: Tab delimited text files showing the foldchanges and p values of the differentially expressed genes	Retina		For each RNA sample three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN ≥9.5 and A260/280 ≥1.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer’s protocol.		tissue:Retina\|strain:AB\|age:2 mpf KO	GSM4861208	GSM4861208: nrl R1; Danio rerio; RNA Seq	GSM4861208		1	For each RNA sample three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN ≥9.5 and A260/280 ≥1.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer's protocol.	GEO Accession:GSM4861208	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP288615		nrl-R1_combined_R1.fastq.gz nrl-R1_combined_R2.fastq.gz	fastq fastq	6989998200.0	23299994.0	GSM4861208 r1	0:150 1:150	A:1947895730;C:1539849390;G:1551787456;T:1950215842;N:249782	150	150	1947895730	1539849390	1551787456	1950215842	249782	SRX9364742	SRS7586957	SRA1147909	GEO	College of Life Science and Technology, Huazhong University of Science and Technology	2	0.90616	0.9059	0.15209	0.15341	0.68998	0.69885	0.49879	0.49931	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc_generic	bulk	bulk	China	2020-10-26	Juvenile	Juvenile	Eye	Sensory System
61645	61645	SRR12899694	SRX9364741	SRS7586956	SRP288615	PRJNA672100	Nrl dependent and independent rod photoreceptor development in zebrafish [RNA Seq]	GSE160138	Transcriptome Analysis	NRL Neural retina leucine zipper is a key regulator of the fate determination and gene expression of rod photoreceptors in the retina of many vertebrates. In this study we observed a unique retinal phenotype in the nrl knockout zebrafish model characterized by reduced rods with shortened outer segments and gradually increased green cones in maturity. By tracing and comparing the developmental processes of WT and nrl knockout rods we found there might be two waves of rod genesis distinguished as nrl dependent and independent with different starting times. To reveal the underlying cellular and molecular mechanisms bulk and single cell RNA seq were performed. The changes in gene expression and cell proportion of rods and cones agreed well with our histological and immunofluorescence studies. Interestingly we found that rods exhibited noticeable heterogeneities in the gene expression patterns and a part of rods in nrl knockout zebrafish misexpressed the green cone genes reflecting a hybrid status of rod and green cone. Furthermore we identified mafba as a novel regulator of rod genesis which was responsible for the development of rods in nrl knockout zebrafish. Our study will largely improve the current understanding of the developmental processes and regulatory mechanisms of rods in zebrafish and probably other species and may facilitate future studies in the fields of retinal development and retinal degeneration. Overall design: Two WT and two nrl KO samples two biological replicates were analyzed. Each sample represented a pool of RNAs from three zebrafish retinas at the age of 2 month. The differentially expressed genes between WT and nrl KO groups were identified.	parent bioproject:PRJNA672094	pubmed:35245286	WT R2	GSM4861207	source name:Retina\|tissue:Retina\|strain:AB\|age:2 mpf type	WT R2	Quality control mapping and expression analysis: Image analysis and base calling were conducted by the HiSeq Control Software HCS + OLB + GAPipeline 1.6 Illumina on the HiSeq instrument. The high quality clean data were generated by Trimmomatic v0.30 and aligned to the reference genome of zebrafish via software Hisat2 v2.0.1. Differential expression analysis: Gene and isoform expression levels were estimated by HTSeq v0.6.1. Differential expression analysis was performed by DESeq Bioconductor package. post adjusted by Benjamini and Hochberg’s approach for controlling the false discovery rate the threshold of p values was set to <0.05 to detect differentially expressed genes. GO and KEGG enrichment analysis: GO TermFinder was used identifying Gene Ontology GO terms that annotate a list of enriched genes with a significant p value less than 0.05. KEGG Kyoto Encyclopedia of Genes and Genomes is a collection of databases dealing with genomes biological pathways diseases drugs and chemical substances http://en.wikipedia.org/wiki/KEGG which was used to enrich significant differential expression gene in KEGG pathways. Genome build: GRCz11 from Ensembl Supplementary files format and content: Tab delimited text files including the raw counts and FPKM values for each Sample Supplementary files format and content: Tab delimited text files showing the foldchanges and p values of the differentially expressed genes	Retina		For each RNA sample three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN ≥9.5 and A260/280 ≥1.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer’s protocol.		tissue:Retina\|strain:AB\|age:2 mpf type	GSM4861207	GSM4861207: WT R2; Danio rerio; RNA Seq	GSM4861207		1	For each RNA sample three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN ≥9.5 and A260/280 ≥1.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer's protocol.	GEO Accession:GSM4861207	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP288615		WT-R2_combined_R1.fastq.gz WT-R2_combined_R2.fastq.gz	fastq fastq	7066558200.0	23555194.0	GSM4861207 r1	0:150 1:150	A:1911018201;C:1615965707;G:1630234641;T:1909071420;N:268231	150	150	1911018201	1615965707	1630234641	1909071420	268231	SRX9364741	SRS7586956	SRA1147909	GEO	College of Life Science and Technology, Huazhong University of Science and Technology	2	0.91673	0.91647	0.11542	0.11684	0.68781	0.69637	0.48784	0.49134	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc_generic	bulk	bulk	China	2020-10-26	Juvenile	Juvenile	Eye	Sensory System
61646	61646	SRR12899693	SRX9364740	SRS7586955	SRP288615	PRJNA672100	Nrl dependent and independent rod photoreceptor development in zebrafish [RNA Seq]	GSE160138	Transcriptome Analysis	NRL Neural retina leucine zipper is a key regulator of the fate determination and gene expression of rod photoreceptors in the retina of many vertebrates. In this study we observed a unique retinal phenotype in the nrl knockout zebrafish model characterized by reduced rods with shortened outer segments and gradually increased green cones in maturity. By tracing and comparing the developmental processes of WT and nrl knockout rods we found there might be two waves of rod genesis distinguished as nrl dependent and independent with different starting times. To reveal the underlying cellular and molecular mechanisms bulk and single cell RNA seq were performed. The changes in gene expression and cell proportion of rods and cones agreed well with our histological and immunofluorescence studies. Interestingly we found that rods exhibited noticeable heterogeneities in the gene expression patterns and a part of rods in nrl knockout zebrafish misexpressed the green cone genes reflecting a hybrid status of rod and green cone. Furthermore we identified mafba as a novel regulator of rod genesis which was responsible for the development of rods in nrl knockout zebrafish. Our study will largely improve the current understanding of the developmental processes and regulatory mechanisms of rods in zebrafish and probably other species and may facilitate future studies in the fields of retinal development and retinal degeneration. Overall design: Two WT and two nrl KO samples two biological replicates were analyzed. Each sample represented a pool of RNAs from three zebrafish retinas at the age of 2 month. The differentially expressed genes between WT and nrl KO groups were identified.	parent bioproject:PRJNA672094	pubmed:35245286	WT R1	GSM4861206	source name:Retina\|tissue:Retina\|strain:AB\|age:2 mpf type	WT R1	Quality control mapping and expression analysis: Image analysis and base calling were conducted by the HiSeq Control Software HCS + OLB + GAPipeline 1.6 Illumina on the HiSeq instrument. The high quality clean data were generated by Trimmomatic v0.30 and aligned to the reference genome of zebrafish via software Hisat2 v2.0.1. Differential expression analysis: Gene and isoform expression levels were estimated by HTSeq v0.6.1. Differential expression analysis was performed by DESeq Bioconductor package. post adjusted by Benjamini and Hochberg’s approach for controlling the false discovery rate the threshold of p values was set to <0.05 to detect differentially expressed genes. GO and KEGG enrichment analysis: GO TermFinder was used identifying Gene Ontology GO terms that annotate a list of enriched genes with a significant p value less than 0.05. KEGG Kyoto Encyclopedia of Genes and Genomes is a collection of databases dealing with genomes biological pathways diseases drugs and chemical substances http://en.wikipedia.org/wiki/KEGG which was used to enrich significant differential expression gene in KEGG pathways. Genome build: GRCz11 from Ensembl Supplementary files format and content: Tab delimited text files including the raw counts and FPKM values for each Sample Supplementary files format and content: Tab delimited text files showing the foldchanges and p values of the differentially expressed genes	Retina		For each RNA sample three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN ≥9.5 and A260/280 ≥1.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer’s protocol.		tissue:Retina\|strain:AB\|age:2 mpf type	GSM4861206	GSM4861206: WT R1; Danio rerio; RNA Seq	GSM4861206		1	For each RNA sample three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN ≥9.5 and A260/280 ≥1.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer's protocol.	GEO Accession:GSM4861206	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP288615		WT-R1_combined_R1.fastq.gz WT-R1_combined_R2.fastq.gz	fastq fastq	6933407700.0	23111359.0	GSM4861206 r1	0:150 1:150	A:1917552178;C:1542500715;G:1553125711;T:1919988847;N:240249	150	150	1917552178	1542500715	1553125711	1919988847	240249	SRX9364740	SRS7586955	SRA1147909	GEO	College of Life Science and Technology, Huazhong University of Science and Technology	2	0.90701	0.90456	0.14405	0.14325	0.68335	0.69221	0.49207	0.4926	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	sc_generic	bulk	bulk	China	2020-10-26	Juvenile	Juvenile	Eye	Sensory System
64385	64385	SRR14679147	SRX11017528	SRS9089834	SRP321802	PRJNA733247	Danio rerio breed:Danio Raw sequence reads	PRJNA733247	Whole Genome Sequencing	zebrafish muscle tissue for scRNA seq and bulk RNA seq			Model organism or animal sample from Danio rerio	zebrafish	breed:Danio\|dev stage:60 day\|sex:missing\|tissue:muscle\|BioSampleModel:Model organism or animal									bulk RNA seq	runx2b+/+ 2 bulk RNA seq	runx2b+/+ 2 bulk RNA seq	tail muscle with intermuscular bone			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP321802		WT_2_60dpf.R1.fq.gz WT_2_60dpf.R2.fq.gz	fastq fastq	7007750400.0	23359168.0	WT 2 60dpf.R1.fq.gz	0:150 1:150	A:1714498514;C:1702913716;G:1897215939;T:1693105532;N:16699	150	150	1714498514	1702913716	1897215939	1693105532	16699	SRX11017528	SRS9089834	SRA1238123	Huazhong Agricultural university\|Huazhong Agricultural university	Huazhong Agricultural university	2	0.93184	0.92606	0.01222	0.01169	0.84762	0.85033	0.67174	0.64259	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2021-05-28	Juvenile	Juvenile	Muscle	Muscular System
64386	64386	SRR14679148	SRX11017527	SRS9089834	SRP321802	PRJNA733247	Danio rerio breed:Danio Raw sequence reads	PRJNA733247	Whole Genome Sequencing	zebrafish muscle tissue for scRNA seq and bulk RNA seq			Model organism or animal sample from Danio rerio	zebrafish	breed:Danio\|dev stage:60 day\|sex:missing\|tissue:muscle\|BioSampleModel:Model organism or animal									bulk RNA seq	runx2b+/+ 1 bulk RNA seq	runx2b+/+ 1 bulk RNA seq	tail muscle with intermuscular bone			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP321802		WT_1_60dpf.R1.fq.gz WT_1_60dpf.R2.fq.gz	fastq fastq	6785203800.0	22617346.0	WT 1 60dpf.R1.fq.gz	0:150 1:150	A:1660992152;C:1637869425;G:1843210897;T:1643114944;N:16382	150	150	1660992152	1637869425	1843210897	1643114944	16382	SRX11017527	SRS9089834	SRA1238123	Huazhong Agricultural university\|Huazhong Agricultural university	Huazhong Agricultural university	2	0.92764	0.92197	0.00968	0.00947	0.84323	0.84577	0.65455	0.6592	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2021-05-28	Juvenile	Juvenile	Muscle	Muscular System
64387	64387	SRR14679149	SRX11017526	SRS9089834	SRP321802	PRJNA733247	Danio rerio breed:Danio Raw sequence reads	PRJNA733247	Whole Genome Sequencing	zebrafish muscle tissue for scRNA seq and bulk RNA seq			Model organism or animal sample from Danio rerio	zebrafish	breed:Danio\|dev stage:60 day\|sex:missing\|tissue:muscle\|BioSampleModel:Model organism or animal									scRNA seq	runx2b / scRNA seq	runx2b / scRNA seq	tail muscle without xxx bone			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP321802		MU_S2_L003_R1_001.fastq.gz MU_S2_L003_R2_001.fastq.gz	fastq fastq	112565768100.0	375219227.0	MU S2 L003 R1 001.fastq.gz	0:150 1:150	A:34329910863;C:17430450121;G:18090145246;T:42713500460;N:1761410	150	150	34329910863	17430450121	18090145246	42713500460	1761410	SRX11017526	SRS9089834	SRA1238123	Huazhong Agricultural university\|Huazhong Agricultural university	Huazhong Agricultural university	2	0.34692	0.92476	0.05138	0.09375	0.98543	0.82371	0.68433	0.7376	150	150	B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	bulk	bulk	China	2021-05-29	Juvenile	Juvenile	Muscle	Muscular System
64388	64388	SRR14679150	SRX11017525	SRS9089834	SRP321802	PRJNA733247	Danio rerio breed:Danio Raw sequence reads	PRJNA733247	Whole Genome Sequencing	zebrafish muscle tissue for scRNA seq and bulk RNA seq			Model organism or animal sample from Danio rerio	zebrafish	breed:Danio\|dev stage:60 day\|sex:missing\|tissue:muscle\|BioSampleModel:Model organism or animal									scRNA seq	runx2b+/+ scRNA seq	runx2b+/+ scRNA seq	tail muscle with intermuscular bone			RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP321802		WT_S1_L003_R1_001.fastq.gz WT_S1_L003_R2_001.fastq.gz	fastq fastq	99838157100.0	332793857.0	WT S1 L003 R1 001.fastq.gz	0:150 1:150	A:30283010374;C:15529232903;G:16181518775;T:37842782328;N:1612720	150	150	30283010374	15529232903	16181518775	37842782328	1612720	SRX11017525	SRS9089834	SRA1238123	Huazhong Agricultural university\|Huazhong Agricultural university	Huazhong Agricultural university	2	0.34302	0.92611	0.04637	0.09453	0.98701	0.83658	0.71917	0.76074	150	150	B	B	mate1-mate2 similar by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	bulk	bulk	China	2021-05-29	Juvenile	Juvenile	Muscle	Muscular System
64389	64389	SRR14679151	SRX11017524	SRS9089834	SRP321802	PRJNA733247	Danio rerio breed:Danio Raw sequence reads	PRJNA733247	Whole Genome Sequencing	zebrafish muscle tissue for scRNA seq and bulk RNA seq			Model organism or animal sample from Danio rerio	zebrafish	breed:Danio\|dev stage:60 day\|sex:missing\|tissue:muscle\|BioSampleModel:Model organism or animal									bulk RNA seq	runx2b / 3 bulk RNA seq	runx2b / 3 bulk RNA seq	tail muscle without xxx bone			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP321802		MUT_3_60dpf.R1.fq.gz MUT_3_60dpf.R2.fq.gz	fastq fastq	7358370600.0	24527902.0	MUT 3 60dpf.R1.fq.gz	0:150 1:150	A:1781646726;C:1790446433;G:2025455441;T:1760804227;N:17773	150	150	1781646726	1790446433	2025455441	1760804227	17773	SRX11017524	SRS9089834	SRA1238123	Huazhong Agricultural university\|Huazhong Agricultural university	Huazhong Agricultural university	2	0.92552	0.9218	0.01223	0.01223	0.86222	0.86348	0.68246	0.64029	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2021-05-28	Juvenile	Juvenile	Muscle	Muscular System
64390	64390	SRR14679152	SRX11017523	SRS9089834	SRP321802	PRJNA733247	Danio rerio breed:Danio Raw sequence reads	PRJNA733247	Whole Genome Sequencing	zebrafish muscle tissue for scRNA seq and bulk RNA seq			Model organism or animal sample from Danio rerio	zebrafish	breed:Danio\|dev stage:60 day\|sex:missing\|tissue:muscle\|BioSampleModel:Model organism or animal									bulk RNA seq	runx2b / 2 bulk RNA seq	runx2b / 2 bulk RNA seq	tail muscle without xxx bone			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP321802		MUT_2_60dpf.R1.fq.gz MUT_2_60dpf.R2.fq.gz	fastq fastq	5983046100.0	19943487.0	MUT 2 60dpf.R1.fq.gz	0:150 1:150	A:1456794159;C:1460953692;G:1613536834;T:1451747111;N:14304	150	150	1456794159	1460953692	1613536834	1451747111	14304	SRX11017523	SRS9089834	SRA1238123	Huazhong Agricultural university\|Huazhong Agricultural university	Huazhong Agricultural university	2	0.93491	0.9294	0.01148	0.01117	0.85474	0.85667	0.69448	0.63383	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2021-05-28	Juvenile	Juvenile	Muscle	Muscular System
64391	64391	SRR14679153	SRX11017522	SRS9089834	SRP321802	PRJNA733247	Danio rerio breed:Danio Raw sequence reads	PRJNA733247	Whole Genome Sequencing	zebrafish muscle tissue for scRNA seq and bulk RNA seq			Model organism or animal sample from Danio rerio	zebrafish	breed:Danio\|dev stage:60 day\|sex:missing\|tissue:muscle\|BioSampleModel:Model organism or animal									bulk RNA seq	runx2b / 1 bulk RNA seq	runx2b / 1 bulk RNA seq	tail muscle without xxx bone			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP321802		MUT_1_60dpf.R1.fq.gz MUT_1_60dpf.R2.fq.gz	fastq fastq	6876053100.0	22920177.0	MUT 1 60dpf.R1.fq.gz	0:150 1:150	A:1683687632;C:1665466650;G:1862910858;T:1663971371;N:16589	150	150	1683687632	1665466650	1862910858	1663971371	16589	SRX11017522	SRS9089834	SRA1238123	Huazhong Agricultural university\|Huazhong Agricultural university	Huazhong Agricultural university	2	0.93272	0.92802	0.01179	0.01133	0.84861	0.84993	0.62206	0.67726	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2021-05-28	Juvenile	Juvenile	Muscle	Muscular System
64392	64392	SRR14679154	SRX11017521	SRS9089834	SRP321802	PRJNA733247	Danio rerio breed:Danio Raw sequence reads	PRJNA733247	Whole Genome Sequencing	zebrafish muscle tissue for scRNA seq and bulk RNA seq			Model organism or animal sample from Danio rerio	zebrafish	breed:Danio\|dev stage:60 day\|sex:missing\|tissue:muscle\|BioSampleModel:Model organism or animal									bulk RNA seq	runx2b+/+ 3 bulk RNA seq	runx2b+/+ 3 bulk RNA seq	tail muscle with intermuscular bone			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP321802		WT_3_60dpf.R1.fq.gz WT_3_60dpf.R2.fq.gz	fastq fastq	6834033900.0	22780113.0	WT 3 60dpf.R1.fq.gz	0:150 1:150	A:1665713519;C:1660512523;G:1864685424;T:1643106338;N:16096	150	150	1665713519	1660512523	1864685424	1643106338	16096	SRX11017521	SRS9089834	SRA1238123	Huazhong Agricultural university\|Huazhong Agricultural university	Huazhong Agricultural university	2	0.92968	0.92349	0.01013	0.01013	0.85811	0.85999	0.62541	0.6776	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc_generic	bulk	bulk	China	2021-05-28	Juvenile	Juvenile	Muscle	Muscular System
76356	76356	SRR24844103	SRX20608301	SRS17908187	SRP441411	PRJNA980839	Adad1 knockout and misense mutant RNAseq	PRJNA980839	Other	The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.			LB023 mutant B	LB023 Mut B	strain:Tuebingen\|age:45dpf\|dev stage:Juvenile\|collection date:2021 03\|geo loc name:USA:Boston\|sex:male\|tissue:Testis\|genotype:Missense MutantB\|BioSampleModel:Model organism or animal									RNAseq of Danio rerio adad1 missense mutant: male testes	LB023 Mut B	LB023 Mut B	Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP441411		LB023-Mut-B_R1_001.fastq.gz LB023-Mut-B_R2_001.fastq.gz	fastq fastq	5532352200.0	18441174.0	LB023 Mut B R1 001.fastq.gz	0:150 1:150	A:1408144772;C:1348146392;G:1440174663;T:1335799503;N:86870	150	150	1408144772	1348146392	1440174663	1335799503	86870	SRX20608301	SRS17908187	SRA1650047	University of Massachusetts Boston\|Biology	University of Massachusetts Boston	2	0.93072	0.9289	0.0921	0.09129	0.73129	0.73143	0.55139	0.54723	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-06-07	Juvenile	Juvenile	Gonad	Reproductive System
76357	76357	SRR24844100	SRX20608300	SRS17908192	SRP441411	PRJNA980839	Adad1 knockout and misense mutant RNAseq	PRJNA980839	Other	The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.			LB023 mutant C	LB023 Mut C	strain:Tuebingen\|age:45dpf\|dev stage:Juvenile\|collection date:2021 03\|geo loc name:USA:Boston\|sex:male\|tissue:Testis\|genotype:Missense MutantC\|BioSampleModel:Model organism or animal									RNAseq of Danio rerio adad1 missense mutant: male testes	LB023 Mut C	LB023 Mut C	Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP441411		LB023-Mut-C_R2_001.fastq.gz LB023-Mut-C_R1_001.fastq.gz	fastq fastq	6159317100.0	20531057.0	LB023 Mut C R1 001.fastq.gz	0:150 1:150	A:1639865405;C:1424690953;G:1522945570;T:1571725037;N:90135	150	150	1639865405	1424690953	1522945570	1571725037	90135	SRX20608300	SRS17908192	SRA1650047	University of Massachusetts Boston\|Biology	University of Massachusetts Boston	2	0.92565	0.92502	0.07339	0.0724	0.70832	0.70924	0.50224	0.49923	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-06-07	Juvenile	Juvenile	Gonad	Reproductive System
76358	76358	SRR24844101	SRX20608299	SRS17908193	SRP441411	PRJNA980839	Adad1 knockout and misense mutant RNAseq	PRJNA980839	Other	The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.			LB023 wildtype sibling control D	LB023 WT D	strain:Tuebingen\|age:45dpf\|dev stage:Juvenile\|collection date:2021 03\|geo loc name:USA:Boston\|sex:male\|tissue:Testis\|genotype:Missense WildtypeD\|BioSampleModel:Model organism or animal									RNAseq of Danio rerio adad1 missense wildtype sibling: male testes	LB023 WT D	LB023 WT D	Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP441411		LB023-WT-D_R2_001.fastq.gz LB023-WT-D_R1_001.fastq.gz	fastq fastq	5436242700.0	18120809.0	LB023 WT D R1 001.fastq.gz	0:150 1:150	A:1448689171;C:1252673824;G:1358298822;T:1376497051;N:83832	150	150	1448689171	1252673824	1358298822	1376497051	83832	SRX20608299	SRS17908193	SRA1650047	University of Massachusetts Boston\|Biology	University of Massachusetts Boston	2	0.91802	0.91762	0.09407	0.09394	0.70916	0.7108	0.54977	0.55217	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-06-07	Juvenile	Juvenile	Gonad	Reproductive System
76359	76359	SRR24844102	SRX20608298	SRS17908191	SRP441411	PRJNA980839	Adad1 knockout and misense mutant RNAseq	PRJNA980839	Other	The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.			adad1 mutant E	adad1 Mut E	strain:Tuebingen\|age:45dpf\|dev stage:Juvenile\|collection date:2021 03\|geo loc name:USA:Boston\|sex:male\|tissue:Testis\|genotype:MutantE\|BioSampleModel:Model organism or animal									RNAseq of Danio rerio adad1 mutant: male testes	adad1 Mut E	adad1 Mut E	Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP441411		adad1-Mut-E_R2_001.fastq.gz adad1-Mut-E_R1_001.fastq.gz	fastq fastq	4958837100.0	16529457.0	adad1 Mut E R1 001.fastq.gz	0:150 1:150	A:1311870356;C:1151609197;G:1254712533;T:1240567756;N:77258	150	150	1311870356	1151609197	1254712533	1240567756	77258	SRX20608298	SRS17908191	SRA1650047	University of Massachusetts Boston\|Biology	University of Massachusetts Boston	2	0.901	0.90124	0.11096	0.11139	0.71851	0.71967	0.5526	0.57121	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-06-07	Juvenile	Juvenile	Gonad	Reproductive System
76360	76360	SRR24844104	SRX20608297	SRS17908190	SRP441411	PRJNA980839	Adad1 knockout and misense mutant RNAseq	PRJNA980839	Other	The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.			adad1 mutant F	adad1 Mut F	strain:Tuebingen\|age:45dpf\|dev stage:Juvenile\|collection date:2021 03\|geo loc name:USA:Boston\|sex:male\|tissue:Testis\|genotype:MutantF\|BioSampleModel:Model organism or animal									RNAseq of Danio rerio adad1 mutant: male testes	adad1 Mut F	adad1 Mut F	Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP441411		adad1-Mut-F_R1_001.fastq.gz adad1-Mut-F_R2_001.fastq.gz	fastq fastq	5780694600.0	19268982.0	adad1 Mut F R1 001.fastq.gz	0:150 1:150	A:1502665613;C:1371103253;G:1490414769;T:1416422204;N:88761	150	150	1502665613	1371103253	1490414769	1416422204	88761	SRX20608297	SRS17908190	SRA1650047	University of Massachusetts Boston\|Biology	University of Massachusetts Boston	2	0.89657	0.89588	0.10966	0.10896	0.72671	0.72728	0.57267	0.55033	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-06-07	Juvenile	Juvenile	Gonad	Reproductive System
76361	76361	SRR24844105	SRX20608296	SRS17908189	SRP441411	PRJNA980839	Adad1 knockout and misense mutant RNAseq	PRJNA980839	Other	The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.			adad1 wildtype sibling control A	adad1 WT A	strain:Tuebingen\|age:45dpf\|dev stage:Juvenile\|collection date:2021 03\|geo loc name:USA:Boston\|sex:male\|tissue:Testis\|genotype:WildtypeA\|BioSampleModel:Model organism or animal									RNAseq of Danio rerio adad1 wildtype sibling: male testes	adad1 WT A	adad1 WT A	Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP441411		adad1-WT-A_R1_001.fastq.gz adad1-WT-A_R2_001.fastq.gz	fastq fastq	8011954200.0	26706514.0	adad1 WT A R1 001.fastq.gz	0:150 1:150	A:2090202005;C:1898897650;G:2026356221;T:1996371474;N:126850	150	150	2090202005	1898897650	2026356221	1996371474	126850	SRX20608296	SRS17908189	SRA1650047	University of Massachusetts Boston\|Biology	University of Massachusetts Boston	2	0.91189	0.91021	0.06102	0.06139	0.68525	0.68718	0.50676	0.50889	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-06-07	Juvenile	Juvenile	Gonad	Reproductive System
76362	76362	SRR24844106	SRX20608295	SRS17908186	SRP441411	PRJNA980839	Adad1 knockout and misense mutant RNAseq	PRJNA980839	Other	The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.			adad1 wildtype sibling control B	adad1 WT B	strain:Tuebingen\|age:45dpf\|dev stage:Juvenile\|collection date:2021 03\|geo loc name:USA:Boston\|sex:male\|tissue:Testis\|genotype:WildtypeB\|BioSampleModel:Model organism or animal									RNAseq of Danio rerio adad1 wildtype sibling: male testes	adad1 WT B	adad1 WT B	Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP441411		adad1-WT-B_R1_001.fastq.gz adad1-WT-B_R2_001.fastq.gz	fastq fastq	7492292100.0	24974307.0	adad1 WT B R1 001.fastq.gz	0:150 1:150	A:1943185783;C:1771813934;G:1904551325;T:1872624369;N:116689	150	150	1943185783	1771813934	1904551325	1872624369	116689	SRX20608295	SRS17908186	SRA1650047	University of Massachusetts Boston\|Biology	University of Massachusetts Boston	2	0.90916	0.90763	0.11162	0.11123	0.67399	0.6743	0.52068	0.52927	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-06-07	Juvenile	Juvenile	Gonad	Reproductive System
76363	76363	SRR24844107	SRX20608294	SRS17908185	SRP441411	PRJNA980839	Adad1 knockout and misense mutant RNAseq	PRJNA980839	Other	The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.			adad1 wildtype sibling control C	adad1 WT C	strain:Tuebingen\|age:45dpf\|dev stage:Juvenile\|collection date:2021 03\|geo loc name:USA:Boston\|sex:male\|tissue:Testis\|genotype:WildtypeC\|BioSampleModel:Model organism or animal									RNAseq of Danio rerio adad1 wildtype sibling: male testes	adad1 WT C	adad1 WT C	Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP441411		adad1-WT-C_R2_001.fastq.gz adad1-WT-C_R1_001.fastq.gz	fastq fastq	7521501900.0	25071673.0	adad1 WT C R1 001.fastq.gz	0:150 1:150	A:1804312038;C:1905161135;G:2076680572;T:1735230886;N:117269	150	150	1804312038	1905161135	2076680572	1735230886	117269	SRX20608294	SRS17908185	SRA1650047	University of Massachusetts Boston\|Biology	University of Massachusetts Boston	2	0.91415	0.91424	0.1126	0.11157	0.72861	0.72924	0.60581	0.59123	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-06-07	Juvenile	Juvenile	Gonad	Reproductive System
76364	76364	SRR24844111	SRX20608293	SRS17908188	SRP441411	PRJNA980839	Adad1 knockout and misense mutant RNAseq	PRJNA980839	Other	The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.			adad1 wildtype sibling control D	adad1 WT D	strain:Tuebingen\|age:45dpf\|dev stage:Juvenile\|collection date:2021 03\|geo loc name:USA:Boston\|sex:male\|tissue:Testis\|genotype:WildtypeD\|BioSampleModel:Model organism or animal									RNAseq of Danio rerio adad1 wildtype sibling: male testes	adad1 WT D	adad1 WT D	Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP441411		adad1-WT-D_R2_001.fastq.gz adad1-WT-D_R1_001.fastq.gz	fastq fastq	6723661500.0	22412205.0	adad1 WT D R1 001.fastq.gz	0:150 1:150	A:1762783841;C:1577461245;G:1700257202;T:1683053935;N:105277	150	150	1762783841	1577461245	1700257202	1683053935	105277	SRX20608293	SRS17908188	SRA1650047	University of Massachusetts Boston\|Biology	University of Massachusetts Boston	2	0.90669	0.90515	0.1057	0.1054	0.7055	0.70648	0.53378	0.53859	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-06-07	Juvenile	Juvenile	Gonad	Reproductive System
76365	76365	SRR24844108	SRX20608292	SRS17908183	SRP441411	PRJNA980839	Adad1 knockout and misense mutant RNAseq	PRJNA980839	Other	The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.			LB023 wildtype sibling control C	LB023 WT C	strain:Tuebingen\|age:45dpf\|dev stage:Juvenile\|collection date:2021 03\|geo loc name:USA:Boston\|sex:male\|tissue:Testis\|genotype:Missense WildtypeC\|BioSampleModel:Model organism or animal									RNAseq of Danio rerio adad1 missense wildtype sibling: male testes	LB023 WT C	LB023 WT C	Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP441411		LB023-WT-C_R1_001.fastq.gz LB023-WT-C_R2_001.fastq.gz	fastq fastq	6931350600.0	23104502.0	LB023 WT C R1 001.fastq.gz	0:150 1:150	A:1738105921;C:1615563430;G:1915220365;T:1662351851;N:109033	150	150	1738105921	1615563430	1915220365	1662351851	109033	SRX20608292	SRS17908183	SRA1650047	University of Massachusetts Boston\|Biology	University of Massachusetts Boston	2	0.85918	0.86008	0.0973	0.0972	0.75621	0.75617	0.51414	0.52127	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-06-07	Juvenile	Juvenile	Gonad	Reproductive System
76366	76366	SRR24844109	SRX20608291	SRS17908182	SRP441411	PRJNA980839	Adad1 knockout and misense mutant RNAseq	PRJNA980839	Other	The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.			LB023 wildtype sibling control B	LB023 WT B	strain:Tuebingen\|age:45dpf\|dev stage:Juvenile\|collection date:2021 03\|geo loc name:USA:Boston\|sex:male\|tissue:Testis\|genotype:Missense WildtypeB\|BioSampleModel:Model organism or animal									RNAseq of Danio rerio adad1 missense wildtype sibling: male testes	LB023 WT B	LB023 WT B	Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP441411		LB023-WT-B_R1_001.fastq.gz LB023-WT-B_R2_001.fastq.gz	fastq fastq	6486567300.0	21621891.0	LB023 WT B R1 001.fastq.gz	0:150 1:150	A:1659315544;C:1565803285;G:1669608945;T:1591739895;N:99631	150	150	1659315544	1565803285	1669608945	1591739895	99631	SRX20608291	SRS17908182	SRA1650047	University of Massachusetts Boston\|Biology	University of Massachusetts Boston	2	0.92214	0.92196	0.09064	0.09079	0.70092	0.70207	0.54638	0.55145	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-06-07	Juvenile	Juvenile	Gonad	Reproductive System
76367	76367	SRR24844110	SRX20608290	SRS17908184	SRP441411	PRJNA980839	Adad1 knockout and misense mutant RNAseq	PRJNA980839	Other	The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.			LB023 wildtype sibling control A	LB023 WT A	strain:Tuebingen\|age:45dpf\|dev stage:Juvenile\|collection date:2021 03\|geo loc name:USA:Boston\|sex:male\|tissue:Testis\|genotype:Missense WildtypeA\|BioSampleModel:Model organism or animal									RNAseq of Danio rerio adad1 missense wildtype sibling: male testes	LB023 WT A	LB023 WT A	Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP441411		LB023-WT-A_R1_001.fastq.gz LB023-WT-A_R2_001.fastq.gz	fastq fastq	7085531700.0	23618439.0	LB023 WT A R1 001.fastq.gz	0:150 1:150	A:1870324648;C:1666204540;G:1769576825;T:1779314498;N:111189	150	150	1870324648	1666204540	1769576825	1779314498	111189	SRX20608290	SRS17908184	SRA1650047	University of Massachusetts Boston\|Biology	University of Massachusetts Boston	2	0.91831	0.91753	0.06037	0.06044	0.70307	0.70368	0.51531	0.51099	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-06-07	Juvenile	Juvenile	Gonad	Reproductive System
76368	76368	SRR24844112	SRX20608289	SRS17908179	SRP441411	PRJNA980839	Adad1 knockout and misense mutant RNAseq	PRJNA980839	Other	The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.			LB023 mutant F	LB023 Mut F	strain:Tuebingen\|age:45dpf\|dev stage:Juvenile\|collection date:2021 03\|geo loc name:USA:Boston\|sex:male\|tissue:Testis\|genotype:Missense MutantF\|BioSampleModel:Model organism or animal									RNAseq of Danio rerio adad1 missense mutant: male testes	LB023 Mut F	LB023 Mut F	Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP441411		LB023-Mut-F_R1_001.fastq.gz LB023-Mut-F_R2_001.fastq.gz	fastq fastq	7753356600.0	25844522.0	LB023 Mut F R1 001.fastq.gz	0:150 1:150	A:2031483621;C:1809017944;G:1970064517;T:1942669709;N:120809	150	150	2031483621	1809017944	1970064517	1942669709	120809	SRX20608289	SRS17908179	SRA1650047	University of Massachusetts Boston\|Biology	University of Massachusetts Boston	2	0.87475	0.87314	0.09092	0.09089	0.75373	0.75434	0.5602	0.56521	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-06-07	Juvenile	Juvenile	Gonad	Reproductive System
76369	76369	SRR24844113	SRX20608288	SRS17908178	SRP441411	PRJNA980839	Adad1 knockout and misense mutant RNAseq	PRJNA980839	Other	The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.			LB023 mutant E	LB023 Mut E	strain:Tuebingen\|age:45dpf\|dev stage:Juvenile\|collection date:2021 03\|geo loc name:USA:Boston\|sex:male\|tissue:Testis\|genotype:Missense MutantE\|BioSampleModel:Model organism or animal									RNAseq of Danio rerio adad1 missense mutant: male testes	LB023 Mut E	LB023 Mut E	Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP441411		LB023-Mut-E_R1_001.fastq.gz LB023-Mut-E_R2_001.fastq.gz	fastq fastq	4532652000.0	15108840.0	LB023 Mut E R1 001.fastq.gz	0:150 1:150	A:1199854650;C:1037858889;G:1150707006;T:1144159494;N:71961	150	150	1199854650	1037858889	1150707006	1144159494	71961	SRX20608288	SRS17908178	SRA1650047	University of Massachusetts Boston\|Biology	University of Massachusetts Boston	2	0.87501	0.87504	0.08393	0.08384	0.76021	0.76055	0.54045	0.54351	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-06-07	Juvenile	Juvenile	Gonad	Reproductive System
76370	76370	SRR24844114	SRX20608287	SRS17908181	SRP441411	PRJNA980839	Adad1 knockout and misense mutant RNAseq	PRJNA980839	Other	The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.			adad1 mutant C	adad1 Mut C	strain:Tuebingen\|age:45dpf\|dev stage:Juvenile\|collection date:2021 03\|geo loc name:USA:Boston\|sex:male\|tissue:Testis\|genotype:MutantC\|BioSampleModel:Model organism or animal									RNAseq of Danio rerio adad1 mutant: male testes	adad1 Mut C	adad1 Mut C	Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP441411		adad1-Mut-C_R1_001.fastq.gz adad1-Mut-C_R2_001.fastq.gz	fastq fastq	7938136500.0	26460455.0	adad1 Mut C R1 001.fastq.gz	0:150 1:150	A:2011717685;C:1935444799;G:2053481206;T:1937375239;N:117571	150	150	2011717685	1935444799	2053481206	1937375239	117571	SRX20608287	SRS17908181	SRA1650047	University of Massachusetts Boston\|Biology	University of Massachusetts Boston	2	0.92456	0.92396	0.08714	0.08738	0.70575	0.70826	0.5441	0.52561	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-06-07	Juvenile	Juvenile	Gonad	Reproductive System
76371	76371	SRR24844115	SRX20608286	SRS17908180	SRP441411	PRJNA980839	Adad1 knockout and misense mutant RNAseq	PRJNA980839	Other	The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.			adad1 mutant A	adad1 Mut A	strain:Tuebingen\|age:45dpf\|dev stage:Juvenile\|collection date:2021 03\|geo loc name:USA:Boston\|sex:male\|tissue:Testis\|genotype:MutantA\|BioSampleModel:Model organism or animal									RNAseq of Danio rerio adad1 mutant: male testes	adad1 Mut A	adad1 Mut A	Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP441411		adad1-Mut-A_R1_001.fastq.gz adad1-Mut-A_R2_001.fastq.gz	fastq fastq	7254148200.0	24180494.0	adad1 Mut A R1 001.fastq.gz	0:150 1:150	A:1849587944;C:1771248935;G:1861148471;T:1772049096;N:113754	150	150	1849587944	1771248935	1861148471	1772049096	113754	SRX20608286	SRS17908180	SRA1650047	University of Massachusetts Boston\|Biology	University of Massachusetts Boston	2	0.93069	0.93108	0.10454	0.10422	0.69899	0.70088	0.53698	0.55029	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	United States	2023-06-07	Juvenile	Juvenile	Gonad	Reproductive System

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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");;