metadata: run_metadata: 86 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "bulk" and tissue

86 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "bulk" and tissue_curation = "Gonad"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.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
24582	24582	SRR25462250	SRX21195051	SRS18453977	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 8mpf 3	GSM7669027	source name:follicle\|strain:AB\|tissue:follicle\|developmental stage:primary growth\|age:8mpf\|genotype:HE cdkn1a +/ \|geo loc name:missing\|collection date:missing	PG HE 8mpf 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:8mpf\|genotype:HE cdkn1a +/	GSM7669027	GSM7669027: PG HE 8mpf 3; Danio rerio; RNA Seq	GSM7669027 r1	GSM7669027	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		HE_PG_8mpf_3_S11_L003_R1_001.fastq.gz HE_PG_8mpf_3_S11_L003_R2_001.fastq.gz	fastq fastq	7161373434.0	60309247.0	GSM7669027 r1	0:59.39 1:59.35	A:1783731260;C:1744025029;G:1733970346;T:1880173306;N:19473493	59	59	1783731260	1744025029	1733970346	1880173306	19473493	SRX21195051	SRS18453977			Karp 12006A, Biology of Vascular Program, Boston Children's Hospital	2	0.94187	0.94592	0.01475	0.01464	0.77447	0.77498	0.45855	0.4635	60	60	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	United States	2023-07-31	Adult	Adult	Gonad	Reproductive System
24583	24583	SRR25462251	SRX21195050	SRS18453976	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 8mpf 2	GSM7669026	source name:follicle\|strain:AB\|tissue:follicle\|developmental stage:primary growth\|age:8mpf\|genotype:HE cdkn1a +/ \|geo loc name:missing\|collection date:missing	PG HE 8mpf 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:8mpf\|genotype:HE cdkn1a +/	GSM7669026	GSM7669026: PG HE 8mpf 2; Danio rerio; RNA Seq	GSM7669026 r1	GSM7669026	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		HE_PG_8mpf_2_S7_L003_R1_001.fastq.gz HE_PG_8mpf_2_S7_L003_R2_001.fastq.gz	fastq fastq	3176994053.0	26828357.0	GSM7669026 r1	0:59.22 1:59.20	A:793619267;C:767135191;G:764404567;T:830643823;N:21191205	59	59	793619267	767135191	764404567	830643823	21191205	SRX21195050	SRS18453976			Karp 12006A, Biology of Vascular Program, Boston Children's Hospital	2	0.93822	0.94226	0.01596	0.0161	0.77684	0.77772	0.47008	0.46904	59	60	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	United States	2023-07-31	Adult	Adult	Gonad	Reproductive System
24584	24584	SRR25462252	SRX21195049	SRS18453975	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 8mpf 1	GSM7669025	source name:follicle\|strain:AB\|tissue:follicle\|developmental stage:primary growth\|age:8mpf\|genotype:HE cdkn1a +/ \|geo loc name:missing\|collection date:missing	PG HE 8mpf 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:8mpf\|genotype:HE cdkn1a +/	GSM7669025	GSM7669025: PG HE 8mpf 1; Danio rerio; RNA Seq	GSM7669025 r1	GSM7669025	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		HE_PG_8mpf_1_S6_L003_R1_001.fastq.gz HE_PG_8mpf_1_S6_L003_R2_001.fastq.gz	fastq fastq	4587580737.0	38590260.0	GSM7669025 r1	0:59.45 1:59.43	A:1149031944;C:1121086335;G:1106925902;T:1203970839;N:6565717	59	59	1149031944	1121086335	1106925902	1203970839	6565717	SRX21195049	SRS18453975			Karp 12006A, Biology of Vascular Program, Boston Children's Hospital	2	0.94032	0.9437	0.01481	0.01462	0.77682	0.77774	0.45843	0.4699	58	60	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	United States	2023-07-31	Adult	Adult	Gonad	Reproductive System
24585	24585	SRR25462253	SRX21195048	SRS18453974	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 8mpf 3	GSM7669024	source name:follicle\|strain:AB\|tissue:follicle\|developmental stage:primary growth\|age:8mpf\|genotype:WT cdkn1a +/+\|geo loc name:missing\|collection date:missing	PG WT 8mpf 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:8mpf\|genotype:WT cdkn1a +/+	GSM7669024	GSM7669024: PG WT 8mpf 3; Danio rerio; RNA Seq	GSM7669024 r1	GSM7669024	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		WT_PG_8mpf_3_S8_L003_R2_001.fastq.gz WT_PG_8mpf_3_S8_L003_R1_001.fastq.gz	fastq fastq	3920821867.0	33089226.0	GSM7669024 r1	0:59.26 1:59.23	A:977738236;C:951999354;G:944769809;T:1023828622;N:22485846	59	59	977738236	951999354	944769809	1023828622	22485846	SRX21195048	SRS18453974			Karp 12006A, Biology of Vascular Program, Boston Children's Hospital	2	0.94193	0.94555	0.01657	0.01646	0.76784	0.76919	0.47238	0.47016	60	60	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	United States	2023-07-31	Adult	Adult	Gonad	Reproductive System
24586	24586	SRR25462254	SRX21195047	SRS18453973	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 8mpf 2	GSM7669023	source name:follicle\|strain:AB\|tissue:follicle\|developmental stage:primary growth\|age:8mpf\|genotype:WT cdkn1a +/+\|geo loc name:missing\|collection date:missing	PG WT 8mpf 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:8mpf\|genotype:WT cdkn1a +/+	GSM7669023	GSM7669023: PG WT 8mpf 2; Danio rerio; RNA Seq	GSM7669023 r1	GSM7669023	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		WT_PG_8mpf_2_S10_L003_R2_001.fastq.gz WT_PG_8mpf_2_S10_L003_R1_001.fastq.gz	fastq fastq	4917868553.0	41430484.0	GSM7669023 r1	0:59.37 1:59.33	A:1231173294;C:1195692797;G:1182545852;T:1292018757;N:16437853	59	59	1231173294	1195692797	1182545852	1292018757	16437853	SRX21195047	SRS18453973			Karp 12006A, Biology of Vascular Program, Boston Children's Hospital	2	0.94048	0.94432	0.0178	0.0178	0.75645	0.7569	0.46332	0.46812	59	57	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	United States	2023-07-31	Adult	Adult	Gonad	Reproductive System
24587	24587	SRR25462255	SRX21195046	SRS18453972	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 8mpf 1	GSM7669022	source name:follicle\|strain:AB\|tissue:follicle\|developmental stage:primary growth\|age:8mpf\|genotype:WT cdkn1a +/+\|geo loc name:missing\|collection date:missing	PG WT 8mpf 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:8mpf\|genotype:WT cdkn1a +/+	GSM7669022	GSM7669022: PG WT 8mpf 1; Danio rerio; RNA Seq	GSM7669022 r1	GSM7669022	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		WT_PG_8mpf_1_S9_L003_R1_001.fastq.gz WT_PG_8mpf_1_S9_L003_R2_001.fastq.gz	fastq fastq	3375380667.0	28408784.0	GSM7669022 r1	0:59.42 1:59.40	A:842316103;C:825987175;G:818715765;T:881225528;N:7136096	59	59	842316103	825987175	818715765	881225528	7136096	SRX21195046	SRS18453972			Karp 12006A, Biology of Vascular Program, Boston Children's Hospital	2	0.94039	0.9444	0.0162	0.01617	0.7697	0.76986	0.47132	0.46938	60	60	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	United States	2023-07-31	Adult	Adult	Gonad	Reproductive System
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
24594	24594	SRR25462243	SRX21195038	SRS18453964	SRP452269	PRJNA1000446	Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish	GSE239623	Transcriptome Analysis	Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.		PV M3	GSM7669033	source name:follicle\|strain:AB\|tissue:follicle\|developmental stage:pre vitellogenin\|genotype:MT ybx1 / \|geo loc name:missing\|collection date:missing	PV M3	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:pre vitellogenin\|genotype:MT ybx1 /	GSM7669033	GSM7669033: PV M3; Danio rerio; RNA Seq	GSM7669033 r1	GSM7669033	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	SRP452269		PV_M3_R1.fastq.gz PV_M3_R2.fastq.gz	fastq fastq	4644457090.0	23465750.0	GSM7669033 r1	0:98.98 1:98.94	A:1196567358;C:1114203322;G:1109379777;T:1223156356;N:1150277	98	98	1196567358	1114203322	1109379777	1223156356	1150277	SRX21195038	SRS18453964			Karp 12006A, Biology of Vascular Program, Boston Children's Hospital	2	0.94849	0.95248	0.02727	0.02708	0.73602	0.73718	0.48396	0.4855	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	United States	2023-07-31	Undetermined	Embryo	Gonad	Reproductive System
24595	24595	SRR25462244	SRX21195037	SRS18453963	SRP452269	PRJNA1000446	Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish	GSE239623	Transcriptome Analysis	Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.		PV M2	GSM7669032	source name:follicle\|strain:AB\|tissue:follicle\|developmental stage:pre vitellogenin\|genotype:MT ybx1 / \|geo loc name:missing\|collection date:missing	PV M2	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:pre vitellogenin\|genotype:MT ybx1 /	GSM7669032	GSM7669032: PV M2; Danio rerio; RNA Seq	GSM7669032 r1	GSM7669032	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	SRP452269		PV_M2_R1.fastq.gz PV_M2_R2.fastq.gz	fastq fastq	2464506276.0	12449948.0	GSM7669032 r1	0:98.99 1:98.96	A:632587002;C:593372099;G:591579950;T:646214108;N:753117	98	98	632587002	593372099	591579950	646214108	753117	SRX21195037	SRS18453963			Karp 12006A, Biology of Vascular Program, Boston Children's Hospital	2	0.94889	0.9522	0.02585	0.02585	0.73669	0.73841	0.48398	0.48486	100	99	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	United States	2023-07-31	Undetermined	Embryo	Gonad	Reproductive System
24596	24596	SRR25462245	SRX21195036	SRS18453962	SRP452269	PRJNA1000446	Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish	GSE239623	Transcriptome Analysis	Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.		PV M1	GSM7669031	source name:follicle\|strain:AB\|tissue:follicle\|developmental stage:pre vitellogenin\|genotype:MT ybx1 / \|geo loc name:missing\|collection date:missing	PV M1	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:pre vitellogenin\|genotype:MT ybx1 /	GSM7669031	GSM7669031: PV M1; Danio rerio; RNA Seq	GSM7669031 r1	GSM7669031	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	SRP452269		PV_M1_R1.fastq.gz PV_M1_R2.fastq.gz	fastq fastq	3634173229.0	18461903.0	GSM7669031 r1	0:98.44 1:98.41	A:930322973;C:875929476;G:875710056;T:948595199;N:3615525	98	98	930322973	875929476	875710056	948595199	3615525	SRX21195036	SRS18453962			Karp 12006A, Biology of Vascular Program, Boston Children's Hospital	2	0.94787	0.95134	0.02457	0.02445	0.73762	0.73843	0.48244	0.48069	100	98	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	United States	2023-07-31	Undetermined	Embryo	Gonad	Reproductive System
24597	24597	SRR25462246	SRX21195035	SRS18453961	SRP452269	PRJNA1000446	Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish	GSE239623	Transcriptome Analysis	Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.		PV WT3	GSM7669030	source name:follicle\|strain:AB\|tissue:follicle\|developmental stage:pre vitellogenin\|genotype:WT ybx1+/+\|geo loc name:missing\|collection date:missing	PV WT3	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:pre vitellogenin\|genotype:WT ybx1+/+	GSM7669030	GSM7669030: PV WT3; Danio rerio; RNA Seq	GSM7669030 r1	GSM7669030	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	SRP452269		PV_WT3_R2.fastq PV_WT3_R1.fastq	fastq fastq	2965772270.0	14976621.0	GSM7669030 r1	0:99.03 1:98.99	A:759343389;C:716154246;G:713466520;T:775995980;N:812135	99	98	759343389	716154246	713466520	775995980	812135	SRX21195035	SRS18453961			Karp 12006A, Biology of Vascular Program, Boston Children's Hospital	2	0.95027	0.95485	0.02356	0.02292	0.74422	0.74554	0.47974	0.48267	100	98	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	United States	2023-07-31	Undetermined	Embryo	Gonad	Reproductive System
24598	24598	SRR25462247	SRX21195034	SRS18453960	SRP452269	PRJNA1000446	Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish	GSE239623	Transcriptome Analysis	Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.		PV WT2	GSM7669029	source name:follicle\|strain:AB\|tissue:follicle\|developmental stage:pre vitellogenin\|genotype:WT ybx1+/+\|geo loc name:missing\|collection date:missing	PV WT2	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:pre vitellogenin\|genotype:WT ybx1+/+	GSM7669029	GSM7669029: PV WT2; Danio rerio; RNA Seq	GSM7669029 r1	GSM7669029	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	SRP452269		PV_WT2_R2.fastq PV_WT2_R1.fastq	fastq fastq	2021387268.0	10195384.0	GSM7669029 r1	0:99.15 1:99.12	A:517788644;C:487363563;G:485168383;T:530550229;N:516449	99	99	517788644	487363563	485168383	530550229	516449	SRX21195034	SRS18453960			Karp 12006A, Biology of Vascular Program, Boston Children's Hospital	2	0.95113	0.9544	0.02394	0.02364	0.74168	0.74363	0.47881	0.47499	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	United States	2023-07-31	Undetermined	Embryo	Gonad	Reproductive System
24599	24599	SRR25462248	SRX21195033	SRS18453959	SRP452269	PRJNA1000446	Genetic Evidence for the Gatekeeping Role of Ybx1 in Controlling Follicle Activation and Early Folliculogenesis by Regulation of Cdkn1a in the Zebrafish	GSE239623	Transcriptome Analysis	Y box binding protein 1 YB 1; Ybx1/ybx1 regulates transcription and translation of targeted genes by DNA/RNA binding. Our previous proteomic study demonstrated a dramatic drop in Ybx1 protein during follicle activation in zebrafish ovary. In this study we created an ybx1 mutant with CRISPR/Cas9 and showed that the folliculogenesis in the mutant ovary ybx1 / was blocked at pre vitellogenic PV to early vitellogenic EV transition leading to small ovaries. The mutant females were therefore sub fertile with reduced fecundity. RNA seq and Western blot analyses identified a variety of genes that showed differential expression between mutant ovary ybx1 / and the control ybx1+/ including cdkn1a p21. Disruption of cdkn1a resulted in embryonic lethality. In p21 heterozygous cdkn1a+/ however follicle activation and maturation in the ovary were both enhanced in contrast to ybx1 mutant ybx1 / . Interestingly partial loss of p21 in heterozygous cdkn1a+/ could rescue the phenotype of ybx1 mutant ybx1 / . Folliculogenesis resumed in ybx1 / ;p21+/ females with normal follicle activation in contrast to the PV EV blockade in ybx1 / mutant. Interestingly the follicle cells from the ybx1 / mutant follicles displayed a poor proliferative activity in vitro; however the cells from the ybx1 / p21+/ follicles resumed normal proliferation compared to that from the wildtype fish. In summary we demonstrated in this study that Ybx1 played a gatekeeping role in controlling PV to EV transition and it might act by suppressing the expression of cdkn1a a cell cycle inhibitor. Overall design: Considering our histological PV to EV follicle blockade we further isolated PV follicles from both WT ybx1+/+ and ybx1 / zebrafish. post RNA isolation we then estbalished bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation we performed sequencing using the Genomics Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.		PV WT1	GSM7669028	source name:follicle\|strain:AB\|tissue:follicle\|developmental stage:pre vitellogenin\|genotype:WT ybx1+/+\|geo loc name:missing\|collection date:missing	PV WT1	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:pre vitellogenin\|genotype:WT ybx1+/+	GSM7669028	GSM7669028: PV WT1; Danio rerio; RNA Seq	GSM7669028 r1	GSM7669028	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	SRP452269		PV_WT1_R1.fastq PV_WT1_R2.fastq	fastq fastq	3244660111.0	16481925.0	GSM7669028 r1	0:98.44 1:98.42	A:831426044;C:781489498;G:779991004;T:848549246;N:3204319	98	98	831426044	781489498	779991004	848549246	3204319	SRX21195033	SRS18453959			Karp 12006A, Biology of Vascular Program, Boston Children's Hospital	2	0.94779	0.95185	0.02328	0.02298	0.74294	0.74391	0.48052	0.47966	95	95	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	United States	2023-07-31	Undetermined	Embryo	Gonad	Reproductive System
30556	30556	SRR27836071	SRX23499420	SRS20351177	SRP487485	PRJNA1072072	Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios	GSE254850	Transcriptome Analysis	Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…	pubmed:38898112	Rbpms2 mApple crosslinked SR3	GSM8059038	source name:Gonad\|tissue:Gonad\|cell type:Germline and somatic\|genotype:Wildtype\|geo loc name:missing\|collection date:missing	Rbpms2 mApple crosslinked SR3	Basespace illumina platform was used and reads were mapped using tophate2 aligner. Estimation of reference genes and transcript was done using cufflinks and reads were mapped to the genome GRCz10. Reads were aligned with the TopHat Alignment App. GRCz10 CSV file that compiled includes tracking ids gene loci and FPKMs for each samples CSV files include tracking and gene id gene short name tss id locus and FPKM for each sample	Gonad		RNA was extracted with an Rneasy Mini Kit Qiagen 74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina 20020589		tissue:Gonad\|cell type:Germline and somatic\|genotype:Wildtype	GSM8059038	GSM8059038: Rbpms2 mApple crosslinked SR3; Danio rerio; RNA Seq	GSM8059038 r1	GSM8059038	1	RNA was extracted with an Rneasy Mini Kit Qiagen 74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina 20020589		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP487485		SR-3_S4_L001_R1_001.fastq.gz SR-3_S4_L001_R2_001.fastq.gz	fastq fastq	588252864.0	3949222.0	GSM8059038 r1	0:74.42 1:74.53	A:116383167;C:176622592;G:176850622;T:118306997;N:89486	74	74	116383167	176622592	176850622	118306997	89486	SRX23499420	SRS20351177	SRA1796363	Marlow, CDRB, Icahn School of Medicine Mount Sinai	Marlow, CDRB, Icahn School of Medicine Mount Sinai												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2024-02-01	Undetermined	Undetermined	Gonad	Reproductive System
30557	30557	SRR27836072	SRX23499419	SRS20351178	SRP487485	PRJNA1072072	Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios	GSE254850	Transcriptome Analysis	Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…	pubmed:38898112	Rbpms2 mApple uncrosslinked SR2	GSM8059037	source name:Gonad\|tissue:Gonad\|cell type:Germline and somatic\|genotype:Wildtype\|geo loc name:missing\|collection date:missing	Rbpms2 mApple uncrosslinked SR2	Basespace illumina platform was used and reads were mapped using tophate2 aligner. Estimation of reference genes and transcript was done using cufflinks and reads were mapped to the genome GRCz10. Reads were aligned with the TopHat Alignment App. GRCz10 CSV file that compiled includes tracking ids gene loci and FPKMs for each samples CSV files include tracking and gene id gene short name tss id locus and FPKM for each sample	Gonad		RNA was extracted with an Rneasy Mini Kit Qiagen 74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina 20020589		tissue:Gonad\|cell type:Germline and somatic\|genotype:Wildtype	GSM8059037	GSM8059037: Rbpms2 mApple uncrosslinked SR2; Danio rerio; RNA Seq	GSM8059037 r1	GSM8059037	1	RNA was extracted with an Rneasy Mini Kit Qiagen 74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina 20020589		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP487485		SR-2_S3_L001_R1_001.fastq.gz SR-2_S3_L001_R2_001.fastq.gz	fastq fastq	547329260.0	3670350.0	GSM8059037 r1	0:74.51 1:74.61	A:109193152;C:163365002;G:162344228;T:112378069;N:48809	74	74	109193152	163365002	162344228	112378069	48809	SRX23499419	SRS20351178	SRA1796363	Marlow, CDRB, Icahn School of Medicine Mount Sinai	Marlow, CDRB, Icahn School of Medicine Mount Sinai												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2024-02-01	Undetermined	Undetermined	Gonad	Reproductive System
30558	30558	SRR27836073	SRX23499418	SRS20351176	SRP487485	PRJNA1072072	Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios	GSE254850	Transcriptome Analysis	Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…	pubmed:38898112	mApple control crosslinked SR8	GSM8059036	source name:Gonad\|tissue:Gonad\|cell type:Germline and somatic\|genotype:Wildtype\|geo loc name:missing\|collection date:missing	mApple control crosslinked SR8	Basespace illumina platform was used and reads were mapped using tophate2 aligner. Estimation of reference genes and transcript was done using cufflinks and reads were mapped to the genome GRCz10. Reads were aligned with the TopHat Alignment App. GRCz10 CSV file that compiled includes tracking ids gene loci and FPKMs for each samples CSV files include tracking and gene id gene short name tss id locus and FPKM for each sample	Gonad		RNA was extracted with an Rneasy Mini Kit Qiagen 74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina 20020589		tissue:Gonad\|cell type:Germline and somatic\|genotype:Wildtype	GSM8059036	GSM8059036: mApple control crosslinked SR8; Danio rerio; RNA Seq	GSM8059036 r1	GSM8059036	1	RNA was extracted with an Rneasy Mini Kit Qiagen 74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina 20020589		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP487485		SR-8_S6_L001_R1_001.fastq.gz SR-8_S6_L001_R2_001.fastq.gz	fastq fastq	474378287.0	3180744.0	GSM8059036 r1	0:74.52 1:74.62	A:90310344;C:145884340;G:146185172;T:91942086;N:56345	74	74	90310344	145884340	146185172	91942086	56345	SRX23499418	SRS20351176	SRA1796363	Marlow, CDRB, Icahn School of Medicine Mount Sinai	Marlow, CDRB, Icahn School of Medicine Mount Sinai												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2024-02-01	Undetermined	Undetermined	Gonad	Reproductive System
30559	30559	SRR27836074	SRX23499417	SRS20351175	SRP487485	PRJNA1072072	Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios	GSE254850	Transcriptome Analysis	Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…	pubmed:38898112	mApple control uncrosslinked SR6	GSM8059035	source name:Gonad\|tissue:Gonad\|cell type:Germline and somatic\|genotype:Wildtype\|geo loc name:missing\|collection date:missing	mApple control uncrosslinked SR6	Basespace illumina platform was used and reads were mapped using tophate2 aligner. Estimation of reference genes and transcript was done using cufflinks and reads were mapped to the genome GRCz10. Reads were aligned with the TopHat Alignment App. GRCz10 CSV file that compiled includes tracking ids gene loci and FPKMs for each samples CSV files include tracking and gene id gene short name tss id locus and FPKM for each sample	Gonad		RNA was extracted with an Rneasy Mini Kit Qiagen 74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina 20020589		tissue:Gonad\|cell type:Germline and somatic\|genotype:Wildtype	GSM8059035	GSM8059035: mApple control uncrosslinked SR6; Danio rerio; RNA Seq	GSM8059035 r1	GSM8059035	1	RNA was extracted with an Rneasy Mini Kit Qiagen 74104 Libraries were generated with an Illumina Truseq RNA Library Prep kit Illumina 20020589		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP487485		SR-6_S5_L001_R1_001.fastq.gz SR-6_S5_L001_R2_001.fastq.gz	fastq fastq	1667210566.0	11187841.0	GSM8059035 r1	0:74.46 1:74.56	A:348153529;C:480420209;G:474792496;T:363567978;N:276354	74	74	348153529	480420209	474792496	363567978	276354	SRX23499417	SRS20351175	SRA1796363	Marlow, CDRB, Icahn School of Medicine Mount Sinai	Marlow, CDRB, Icahn School of Medicine Mount Sinai												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2024-02-01	Undetermined	Undetermined	Gonad	Reproductive System
30560	30560	SRR27836075	SRX23499416	SRS20351174	SRP487485	PRJNA1072072	Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios	GSE254850	Transcriptome Analysis	Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…	pubmed:38898112	rbpms2 mutant 4 21 dpf	GSM8059034	source name:Gonad\|tissue:Gonad\|cell type:Germline and somatic\|genotype:rbpms2a ae30; rbpms2b sa MM\|geo loc name:missing\|collection date:missing	rbpms2 mutant 4 21 dpf	Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample	Gonad		RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947		tissue:Gonad\|cell type:Germline and somatic\|genotype:rbpms2a ae30; rbpms2b sa MM	GSM8059034	GSM8059034: rbpms2 mutant 4 21 dpf; Danio rerio; RNA Seq	GSM8059034 r1	GSM8059034	1	RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP487485	loader:fastq load.py	rbpms2-d21-DM_4_S8_L001_R1_001.fastq.gz rbpms2-d21-DM_4_S8_L001_R2_001.fastq.gz	fastq fastq	2533252722.0	24835811.0	GSM8059034 r1	0:51 1:51	A:767895104;C:496128064;G:502250517;T:766951391;N:27646	51	51	767895104	496128064	502250517	766951391	27646	SRX23499416	SRS20351174	SRA1796363	Marlow, CDRB, Icahn School of Medicine Mount Sinai	Marlow, CDRB, Icahn School of Medicine Mount Sinai												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	United States	2024-02-01	Larval	Larval	Gonad	Reproductive System
30561	30561	SRR27836076	SRX23499416	SRS20351174	SRP487485	PRJNA1072072	Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios	GSE254850	Transcriptome Analysis	Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…	pubmed:38898112	rbpms2 mutant 4 21 dpf	GSM8059034	source name:Gonad\|tissue:Gonad\|cell type:Germline and somatic\|genotype:rbpms2a ae30; rbpms2b sa MM\|geo loc name:missing\|collection date:missing	rbpms2 mutant 4 21 dpf	Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample	Gonad		RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947		tissue:Gonad\|cell type:Germline and somatic\|genotype:rbpms2a ae30; rbpms2b sa MM	GSM8059034	GSM8059034: rbpms2 mutant 4 21 dpf; Danio rerio; RNA Seq	GSM8059034 r1	GSM8059034	1	RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP487485	loader:fastq load.py	rbpms2-d21-DM_4_S8_L002_R1_001.fastq.gz rbpms2-d21-DM_4_S8_L002_R2_001.fastq.gz	fastq fastq	2500214514.0	24511907.0	GSM8059034 r2	0:51 1:51	A:757980090;C:489633622;G:495839519;T:756737989;N:23294	51	51	757980090	489633622	495839519	756737989	23294	SRX23499416	SRS20351174	SRA1796363	Marlow, CDRB, Icahn School of Medicine Mount Sinai	Marlow, CDRB, Icahn School of Medicine Mount Sinai												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	United States	2024-02-01	Larval	Larval	Gonad	Reproductive System
30562	30562	SRR27836077	SRX23499415	SRS20351173	SRP487485	PRJNA1072072	Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios	GSE254850	Transcriptome Analysis	Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…	pubmed:38898112	rbpms2 mutant 3 21 dpf	GSM8059033	source name:Gonad\|tissue:Gonad\|cell type:Germline and somatic\|genotype:rbpms2a ae30; rbpms2b sa MM\|geo loc name:missing\|collection date:missing	rbpms2 mutant 3 21 dpf	Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample	Gonad		RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947		tissue:Gonad\|cell type:Germline and somatic\|genotype:rbpms2a ae30; rbpms2b sa MM	GSM8059033	GSM8059033: rbpms2 mutant 3 21 dpf; Danio rerio; RNA Seq	GSM8059033 r1	GSM8059033	1	RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP487485	loader:fastq load.py	rbpms2-d21-DM_3_S7_L001_R1_001.fastq.gz rbpms2-d21-DM_3_S7_L001_R2_001.fastq.gz	fastq fastq	2383569354.0	23368327.0	GSM8059033 r1	0:51 1:51	A:705650487;C:468856307;G:473479720;T:735556568;N:26272	51	51	705650487	468856307	473479720	735556568	26272	SRX23499415	SRS20351173	SRA1796363	Marlow, CDRB, Icahn School of Medicine Mount Sinai	Marlow, CDRB, Icahn School of Medicine Mount Sinai												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	United States	2024-02-01	Larval	Larval	Gonad	Reproductive System
30563	30563	SRR27836078	SRX23499415	SRS20351173	SRP487485	PRJNA1072072	Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios	GSE254850	Transcriptome Analysis	Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…	pubmed:38898112	rbpms2 mutant 3 21 dpf	GSM8059033	source name:Gonad\|tissue:Gonad\|cell type:Germline and somatic\|genotype:rbpms2a ae30; rbpms2b sa MM\|geo loc name:missing\|collection date:missing	rbpms2 mutant 3 21 dpf	Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample	Gonad		RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947		tissue:Gonad\|cell type:Germline and somatic\|genotype:rbpms2a ae30; rbpms2b sa MM	GSM8059033	GSM8059033: rbpms2 mutant 3 21 dpf; Danio rerio; RNA Seq	GSM8059033 r1	GSM8059033	1	RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP487485	loader:fastq load.py	rbpms2-d21-DM_3_S7_L002_R1_001.fastq.gz rbpms2-d21-DM_3_S7_L002_R2_001.fastq.gz	fastq fastq	2324856114.0	22792707.0	GSM8059033 r2	0:51 1:51	A:688232198;C:457346277;G:462034541;T:717221485;N:21613	51	51	688232198	457346277	462034541	717221485	21613	SRX23499415	SRS20351173	SRA1796363	Marlow, CDRB, Icahn School of Medicine Mount Sinai	Marlow, CDRB, Icahn School of Medicine Mount Sinai												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	United States	2024-02-01	Larval	Larval	Gonad	Reproductive System
30564	30564	SRR27836079	SRX23499414	SRS20351172	SRP487485	PRJNA1072072	Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios	GSE254850	Transcriptome Analysis	Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…	pubmed:38898112	rbpms2 mutant 1 21 dpf	GSM8059032	source name:Gonad\|tissue:Gonad\|cell type:Germline and somatic\|genotype:rbpms2a ae30; rbpms2b sa MM\|geo loc name:missing\|collection date:missing	rbpms2 mutant 1 21 dpf	Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample	Gonad		RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947		tissue:Gonad\|cell type:Germline and somatic\|genotype:rbpms2a ae30; rbpms2b sa MM	GSM8059032	GSM8059032: rbpms2 mutant 1 21 dpf; Danio rerio; RNA Seq	GSM8059032 r1	GSM8059032	1	RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP487485	loader:fastq load.py	rbpms2-d21-DM_1_S5_L001_R1_001.fastq.gz rbpms2-d21-DM_1_S5_L001_R2_001.fastq.gz	fastq fastq	2412458100.0	23651550.0	GSM8059032 r1	0:51 1:51	A:726246267;C:465733066;G:465377798;T:755071663;N:29306	51	51	726246267	465733066	465377798	755071663	29306	SRX23499414	SRS20351172	SRA1796363	Marlow, CDRB, Icahn School of Medicine Mount Sinai	Marlow, CDRB, Icahn School of Medicine Mount Sinai												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	United States	2024-02-01	Larval	Larval	Gonad	Reproductive System
30565	30565	SRR27836080	SRX23499414	SRS20351172	SRP487485	PRJNA1072072	Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios	GSE254850	Transcriptome Analysis	Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…	pubmed:38898112	rbpms2 mutant 1 21 dpf	GSM8059032	source name:Gonad\|tissue:Gonad\|cell type:Germline and somatic\|genotype:rbpms2a ae30; rbpms2b sa MM\|geo loc name:missing\|collection date:missing	rbpms2 mutant 1 21 dpf	Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample	Gonad		RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947		tissue:Gonad\|cell type:Germline and somatic\|genotype:rbpms2a ae30; rbpms2b sa MM	GSM8059032	GSM8059032: rbpms2 mutant 1 21 dpf; Danio rerio; RNA Seq	GSM8059032 r1	GSM8059032	1	RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP487485	loader:fastq load.py	rbpms2-d21-DM_1_S5_L002_R1_001.fastq.gz rbpms2-d21-DM_1_S5_L002_R2_001.fastq.gz	fastq fastq	2363898144.0	23175472.0	GSM8059032 r2	0:51 1:51	A:711756208;C:456236364;G:456088591;T:739792903;N:24078	51	51	711756208	456236364	456088591	739792903	24078	SRX23499414	SRS20351172	SRA1796363	Marlow, CDRB, Icahn School of Medicine Mount Sinai	Marlow, CDRB, Icahn School of Medicine Mount Sinai												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	United States	2024-02-01	Larval	Larval	Gonad	Reproductive System
30566	30566	SRR27836081	SRX23499413	SRS20351171	SRP487485	PRJNA1072072	Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios	GSE254850	Transcriptome Analysis	Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…	pubmed:38898112	rbpms2 wildtype 3 21 dpf	GSM8059031	source name:Gonad\|tissue:Gonad\|cell type:Germline and somatic\|genotype:Wildtype\|geo loc name:missing\|collection date:missing	rbpms2 wildtype 3 21 dpf	Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample	Gonad		RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947		tissue:Gonad\|cell type:Germline and somatic\|genotype:Wildtype	GSM8059031	GSM8059031: rbpms2 wildtype 3 21 dpf; Danio rerio; RNA Seq	GSM8059031 r1	GSM8059031	1	RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP487485	loader:fastq load.py	rbpms2-d21-WT_3_S3_L001_R1_001.fastq.gz rbpms2-d21-WT_3_S3_L001_R2_001.fastq.gz	fastq fastq	2048418162.0	20082531.0	GSM8059031 r1	0:51 1:51	A:612611264;C:409068349;G:413909657;T:612805097;N:23795	51	51	612611264	409068349	413909657	612805097	23795	SRX23499413	SRS20351171	SRA1796363	Marlow, CDRB, Icahn School of Medicine Mount Sinai	Marlow, CDRB, Icahn School of Medicine Mount Sinai												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	United States	2024-02-01	Larval	Larval	Gonad	Reproductive System
30567	30567	SRR27836082	SRX23499413	SRS20351171	SRP487485	PRJNA1072072	Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios	GSE254850	Transcriptome Analysis	Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…	pubmed:38898112	rbpms2 wildtype 3 21 dpf	GSM8059031	source name:Gonad\|tissue:Gonad\|cell type:Germline and somatic\|genotype:Wildtype\|geo loc name:missing\|collection date:missing	rbpms2 wildtype 3 21 dpf	Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample	Gonad		RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947		tissue:Gonad\|cell type:Germline and somatic\|genotype:Wildtype	GSM8059031	GSM8059031: rbpms2 wildtype 3 21 dpf; Danio rerio; RNA Seq	GSM8059031 r1	GSM8059031	1	RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP487485	loader:fastq load.py	rbpms2-d21-WT_3_S3_L002_R1_001.fastq.gz rbpms2-d21-WT_3_S3_L002_R2_001.fastq.gz	fastq fastq	2018915070.0	19793285.0	GSM8059031 r2	0:51 1:51	A:603776465;C:403221066;G:408169193;T:603728354;N:19992	51	51	603776465	403221066	408169193	603728354	19992	SRX23499413	SRS20351171	SRA1796363	Marlow, CDRB, Icahn School of Medicine Mount Sinai	Marlow, CDRB, Icahn School of Medicine Mount Sinai												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	United States	2024-02-01	Larval	Larval	Gonad	Reproductive System
30568	30568	SRR27836083	SRX23499412	SRS20351179	SRP487485	PRJNA1072072	Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios	GSE254850	Transcriptome Analysis	Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…	pubmed:38898112	rbpms2 wildtype 2 21 dpf	GSM8059030	source name:Gonad\|tissue:Gonad\|cell type:Germline and somatic\|genotype:Wildtype\|geo loc name:missing\|collection date:missing	rbpms2 wildtype 2 21 dpf	Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample	Gonad		RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947		tissue:Gonad\|cell type:Germline and somatic\|genotype:Wildtype	GSM8059030	GSM8059030: rbpms2 wildtype 2 21 dpf; Danio rerio; RNA Seq	GSM8059030 r1	GSM8059030	1	RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP487485	loader:fastq load.py	rbpms2-d21-WT_2_S2_L001_R1_001.fastq.gz rbpms2-d21-WT_2_S2_L001_R2_001.fastq.gz	fastq fastq	1927777866.0	18899783.0	GSM8059030 r1	0:51 1:51	A:589122616;C:372230241;G:374787285;T:591617780;N:19944	51	51	589122616	372230241	374787285	591617780	19944	SRX23499412	SRS20351179	SRA1796363	Marlow, CDRB, Icahn School of Medicine Mount Sinai	Marlow, CDRB, Icahn School of Medicine Mount Sinai												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	United States	2024-02-01	Larval	Larval	Gonad	Reproductive System
30569	30569	SRR27836084	SRX23499412	SRS20351179	SRP487485	PRJNA1072072	Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios	GSE254850	Transcriptome Analysis	Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…	pubmed:38898112	rbpms2 wildtype 2 21 dpf	GSM8059030	source name:Gonad\|tissue:Gonad\|cell type:Germline and somatic\|genotype:Wildtype\|geo loc name:missing\|collection date:missing	rbpms2 wildtype 2 21 dpf	Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample	Gonad		RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947		tissue:Gonad\|cell type:Germline and somatic\|genotype:Wildtype	GSM8059030	GSM8059030: rbpms2 wildtype 2 21 dpf; Danio rerio; RNA Seq	GSM8059030 r1	GSM8059030	1	RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP487485	loader:fastq load.py	rbpms2-d21-WT_2_S2_L002_R1_001.fastq.gz rbpms2-d21-WT_2_S2_L002_R2_001.fastq.gz	fastq fastq	1901436570.0	18641535.0	GSM8059030 r2	0:51 1:51	A:581077435;C:367152917;G:369822980;T:583366137;N:17101	51	51	581077435	367152917	369822980	583366137	17101	SRX23499412	SRS20351179	SRA1796363	Marlow, CDRB, Icahn School of Medicine Mount Sinai	Marlow, CDRB, Icahn School of Medicine Mount Sinai												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	United States	2024-02-01	Larval	Larval	Gonad	Reproductive System
30570	30570	SRR27836085	SRX23499411	SRS20351170	SRP487485	PRJNA1072072	Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios	GSE254850	Transcriptome Analysis	Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…	pubmed:38898112	rbpms2 wildtype 1 21 dpf	GSM8059029	source name:Gonad\|tissue:Gonad\|cell type:Germline and somatic\|genotype:Wildtype\|geo loc name:missing\|collection date:missing	rbpms2 wildtype 1 21 dpf	Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample	Gonad		RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947		tissue:Gonad\|cell type:Germline and somatic\|genotype:Wildtype	GSM8059029	GSM8059029: rbpms2 wildtype 1 21 dpf; Danio rerio; RNA Seq	GSM8059029 r1	GSM8059029	1	RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP487485	loader:fastq load.py	rbpms2-d21-WT_1_S1_L001_R1_001.fastq.gz rbpms2-d21-WT_1_S1_L001_R2_001.fastq.gz	fastq fastq	1878693222.0	18418561.0	GSM8059029 r1	0:51 1:51	A:581058368;C:356028122;G:360378733;T:581204723;N:23276	51	51	581058368	356028122	360378733	581204723	23276	SRX23499411	SRS20351170	SRA1796363	Marlow, CDRB, Icahn School of Medicine Mount Sinai	Marlow, CDRB, Icahn School of Medicine Mount Sinai												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	United States	2024-02-01	Larval	Larval	Gonad	Reproductive System
30571	30571	SRR27836086	SRX23499411	SRS20351170	SRP487485	PRJNA1072072	Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios	GSE254850	Transcriptome Analysis	Reproductive success relies on proper establishment and maintenance of biological sex. In many animals including mammals the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp Rbpms2 is required for ovary fate in zebrafish. Here we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs which include testis factors and ribosome biogenesis factors. Further genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component Missing oocyte Mios. Cumulatively our findings indicate that early gonocytes are in a dual poised bipotential state in which Rbpms2 acts as a binary fate switch. Specifically Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2 we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential…	pubmed:38898112	rbpms2 wildtype 1 21 dpf	GSM8059029	source name:Gonad\|tissue:Gonad\|cell type:Germline and somatic\|genotype:Wildtype\|geo loc name:missing\|collection date:missing	rbpms2 wildtype 1 21 dpf	Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids symbols counts FPKMs and TPMs for each sample CSV files include gene id symbol count FPKM and TPM for each sample	Gonad		RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947		tissue:Gonad\|cell type:Germline and somatic\|genotype:Wildtype	GSM8059029	GSM8059029: rbpms2 wildtype 1 21 dpf; Danio rerio; RNA Seq	GSM8059029 r1	GSM8059029	1	RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories 634947		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP487485	loader:fastq load.py	rbpms2-d21-WT_1_S1_L002_R1_001.fastq.gz rbpms2-d21-WT_1_S1_L002_R2_001.fastq.gz	fastq fastq	1861916160.0	18254080.0	GSM8059029 r2	0:51 1:51	A:575859972;C:352771580;G:357641601;T:575624138;N:18869	51	51	575859972	352771580	357641601	575624138	18869	SRX23499411	SRS20351170	SRA1796363	Marlow, CDRB, Icahn School of Medicine Mount Sinai	Marlow, CDRB, Icahn School of Medicine Mount Sinai												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	United States	2024-02-01	Larval	Larval	Gonad	Reproductive System
32476	32476	SRR29270149	SRX24787634	SRS21505104	SRP511487	PRJNA1119569	RNA seq of zebrafish foxl2l mutant	PRJNA1119569	Other	Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.			foxl2l Mut 20 1	strain:AB\|age:20\|collection date:2023 06 10\|geo loc name:China\|sex:hermaphrodite\|tissue:gonad\|BioSampleModel:Model organism or animal									foxl2l Mut 20 1	E10	E10	50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	NextSeq 500	SRP511487		foxl2l_Mut-20-1_S162_R1.fastq.gz foxl2l_Mut-20-1_S162_R2.fastq.gz	fastq fastq	8940963680.0	29605840.0	foxl2l Mut 20 1 S162 R1.fastq.gz	0:151 1:151	A:2232167098;C:2229744850;G:2271326718;T:2207692629;N:32385	151	151	2232167098	2229744850	2271326718	2207692629	32385	SRX24787634	SRS21505104	SRA1887976	Institute of Hydrobiology, Chinese Academy of Sciences\|Center for Fish Biology and Fishery Biotechnology	Institute of Hydrobiology, Chinese Academy of Sciences												B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	bulk	bulk	bulk	China	2024-06-03	Undetermined	Undetermined	Gonad	Reproductive System
32477	32477	SRR29270150	SRX24787633	SRS21505103	SRP511487	PRJNA1119569	RNA seq of zebrafish foxl2l mutant	PRJNA1119569	Other	Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.			foxl2l Het 20 3	strain:AB\|age:20\|collection date:2023 06 09\|geo loc name:China\|sex:hermaphrodite\|tissue:gonad\|BioSampleModel:Model organism or animal									foxl2l Het 20 3	E9	E9	50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	NextSeq 500	SRP511487		foxl2l_Het-20-3_S161_R1.fastq.gz foxl2l_Het-20-3_S161_R2.fastq.gz	fastq fastq	7038409282.0	23305991.0	foxl2l Het 20 3 S161 R1.fastq.gz	0:151 1:151	A:1766863186;C:1740008639;G:1787471686;T:1744039429;N:26342	151	151	1766863186	1740008639	1787471686	1744039429	26342	SRX24787633	SRS21505103	SRA1887976	Institute of Hydrobiology, Chinese Academy of Sciences\|Center for Fish Biology and Fishery Biotechnology	Institute of Hydrobiology, Chinese Academy of Sciences												B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	bulk	bulk	bulk	China	2024-06-03	Undetermined	Undetermined	Gonad	Reproductive System
32478	32478	SRR29270151	SRX24787632	SRS21505102	SRP511487	PRJNA1119569	RNA seq of zebrafish foxl2l mutant	PRJNA1119569	Other	Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.			foxl2l Het 20 2	strain:AB\|age:20\|collection date:2023 06 08\|geo loc name:China\|sex:hermaphrodite\|tissue:gonad\|BioSampleModel:Model organism or animal									foxl2l Het 20 2	E8	E8	50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	NextSeq 500	SRP511487		foxl2l_Het-20-2_S160_R1.fastq.gz foxl2l_Het-20-2_S160_R2.fastq.gz	fastq fastq	6772505832.0	22425516.0	foxl2l Het 20 2 S160 R1.fastq.gz	0:151 1:151	A:1704124986;C:1673138074;G:1713003931;T:1682214009;N:24832	151	151	1704124986	1673138074	1713003931	1682214009	24832	SRX24787632	SRS21505102	SRA1887976	Institute of Hydrobiology, Chinese Academy of Sciences\|Center for Fish Biology and Fishery Biotechnology	Institute of Hydrobiology, Chinese Academy of Sciences												B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	bulk	bulk	bulk	China	2024-06-03	Undetermined	Undetermined	Gonad	Reproductive System
32479	32479	SRR29270152	SRX24787631	SRS21505101	SRP511487	PRJNA1119569	RNA seq of zebrafish foxl2l mutant	PRJNA1119569	Other	Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.			foxl2l Het 20 1	strain:AB\|age:20\|collection date:2023 06 07\|geo loc name:China\|sex:hermaphrodite\|tissue:gonad\|BioSampleModel:Model organism or animal									foxl2l Het 20 1	E7	E7	50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	NextSeq 500	SRP511487		foxl2l_Het-20-1_S159_R1.fastq.gz foxl2l_Het-20-1_S159_R2.fastq.gz	fastq fastq	11685740812.0	38694506.0	foxl2l Het 20 1 S159 R1.fastq.gz	0:151 1:151	A:2939618668;C:2888861085;G:2958173208;T:2899044704;N:43147	151	151	2939618668	2888861085	2958173208	2899044704	43147	SRX24787631	SRS21505101	SRA1887976	Institute of Hydrobiology, Chinese Academy of Sciences\|Center for Fish Biology and Fishery Biotechnology	Institute of Hydrobiology, Chinese Academy of Sciences												B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	bulk	bulk	bulk	China	2024-06-03	Undetermined	Undetermined	Gonad	Reproductive System
32480	32480	SRR29270153	SRX24787630	SRS21505100	SRP511487	PRJNA1119569	RNA seq of zebrafish foxl2l mutant	PRJNA1119569	Other	Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.			foxl2l Mut 15 3	strain:AB\|age:15\|collection date:2023 06 06\|geo loc name:China\|sex:hermaphrodite\|tissue:gonad\|BioSampleModel:Model organism or animal									foxl2l Mut 15 3	E6	E6	50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	NextSeq 500	SRP511487		foxl2l_Mut-15-3_S158_R1.fastq.gz foxl2l_Mut-15-3_S158_R2.fastq.gz	fastq fastq	9503789604.0	31469502.0	foxl2l Mut 15 3 S158 R1.fastq.gz	0:151 1:151	A:2393052443;C:2340958111;G:2411502428;T:2358240313;N:36309	151	151	2393052443	2340958111	2411502428	2358240313	36309	SRX24787630	SRS21505100	SRA1887976	Institute of Hydrobiology, Chinese Academy of Sciences\|Center for Fish Biology and Fishery Biotechnology	Institute of Hydrobiology, Chinese Academy of Sciences												B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	bulk	bulk	bulk	China	2024-06-03	Undetermined	Undetermined	Gonad	Reproductive System
32481	32481	SRR29270154	SRX24787629	SRS21505099	SRP511487	PRJNA1119569	RNA seq of zebrafish foxl2l mutant	PRJNA1119569	Other	Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.			foxl2l Mut 15 2	strain:AB\|age:15\|collection date:2023 06 05\|geo loc name:China\|sex:hermaphrodite\|tissue:gonad\|BioSampleModel:Model organism or animal									foxl2l Mut 15 2	E5	E5	50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	NextSeq 500	SRP511487		foxl2l_Mut-15-2_S157_R1.fastq.gz foxl2l_Mut-15-2_S157_R2.fastq.gz	fastq fastq	7416837026.0	24559063.0	foxl2l Mut 15 2 S157 R1.fastq.gz	0:151 1:151	A:1865711045;C:1830489703;G:1881612508;T:1838995980;N:27790	151	151	1865711045	1830489703	1881612508	1838995980	27790	SRX24787629	SRS21505099	SRA1887976	Institute of Hydrobiology, Chinese Academy of Sciences\|Center for Fish Biology and Fishery Biotechnology	Institute of Hydrobiology, Chinese Academy of Sciences												B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	bulk	bulk	bulk	China	2024-06-03	Undetermined	Undetermined	Gonad	Reproductive System
32482	32482	SRR29270155	SRX24787628	SRS21505098	SRP511487	PRJNA1119569	RNA seq of zebrafish foxl2l mutant	PRJNA1119569	Other	Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.			foxl2l Mut 15 1	strain:AB\|age:15\|collection date:2023 06 04\|geo loc name:China\|sex:hermaphrodite\|tissue:gonad\|BioSampleModel:Model organism or animal									foxl2l Mut 15 1	E4	E4	50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	NextSeq 500	SRP511487		foxl2l_Mut-15-1_S156_R1.fastq.gz foxl2l_Mut-15-1_S156_R2.fastq.gz	fastq fastq	7092721868.0	23485834.0	foxl2l Mut 15 1 S156 R1.fastq.gz	0:151 1:151	A:1764166761;C:1770534219;G:1820397492;T:1737597123;N:26273	151	151	1764166761	1770534219	1820397492	1737597123	26273	SRX24787628	SRS21505098	SRA1887976	Institute of Hydrobiology, Chinese Academy of Sciences\|Center for Fish Biology and Fishery Biotechnology	Institute of Hydrobiology, Chinese Academy of Sciences												B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	bulk	bulk	bulk	China	2024-06-03	Undetermined	Undetermined	Gonad	Reproductive System
32483	32483	SRR29270156	SRX24787627	SRS21505097	SRP511487	PRJNA1119569	RNA seq of zebrafish foxl2l mutant	PRJNA1119569	Other	Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.			foxl2l Het 15 3	strain:AB\|age:15\|collection date:2023 06 03\|geo loc name:China\|sex:hermaphrodite\|tissue:gonad\|BioSampleModel:Model organism or animal									foxl2l Het 15 3	E3	E3	50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	NextSeq 500	SRP511487		foxl2l_Het-15-3_S155_R1.fastq.gz foxl2l_Het-15-3_S155_R2.fastq.gz	fastq fastq	8083606820.0	26766910.0	foxl2l Het 15 3 S155 R1.fastq.gz	0:151 1:151	A:2028557443;C:2001113164;G:2050610840;T:2003295953;N:29420	151	151	2028557443	2001113164	2050610840	2003295953	29420	SRX24787627	SRS21505097	SRA1887976	Institute of Hydrobiology, Chinese Academy of Sciences\|Center for Fish Biology and Fishery Biotechnology	Institute of Hydrobiology, Chinese Academy of Sciences												B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	bulk	bulk	bulk	China	2024-06-03	Undetermined	Undetermined	Gonad	Reproductive System
32484	32484	SRR29270157	SRX24787626	SRS21505096	SRP511487	PRJNA1119569	RNA seq of zebrafish foxl2l mutant	PRJNA1119569	Other	Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.			foxl2l Mut 20 3	strain:AB\|age:20\|collection date:2023 06 12\|geo loc name:China\|sex:hermaphrodite\|tissue:gonad\|BioSampleModel:Model organism or animal									foxl2l Mut 20 3	E12	E12	50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	NextSeq 500	SRP511487		foxl2l_Mut-20-3_S164_R1.fastq.gz foxl2l_Mut-20-3_S164_R2.fastq.gz	fastq fastq	7474861796.0	24751198.0	foxl2l Mut 20 3 S164 R1.fastq.gz	0:151 1:151	A:1878881650;C:1849512621;G:1891142525;T:1855296720;N:28280	151	151	1878881650	1849512621	1891142525	1855296720	28280	SRX24787626	SRS21505096	SRA1887976	Institute of Hydrobiology, Chinese Academy of Sciences\|Center for Fish Biology and Fishery Biotechnology	Institute of Hydrobiology, Chinese Academy of Sciences												B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	bulk	bulk	bulk	China	2024-06-03	Undetermined	Undetermined	Gonad	Reproductive System
32485	32485	SRR29270158	SRX24787625	SRS21505095	SRP511487	PRJNA1119569	RNA seq of zebrafish foxl2l mutant	PRJNA1119569	Other	Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.			foxl2l Mut 20 2	strain:AB\|age:20\|collection date:2023 06 11\|geo loc name:China\|sex:hermaphrodite\|tissue:gonad\|BioSampleModel:Model organism or animal									foxl2l Mut 20 2	E11	E11	50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	NextSeq 500	SRP511487		foxl2l_Mut-20-2_S163_R1.fastq.gz foxl2l_Mut-20-2_S163_R2.fastq.gz	fastq fastq	8203704066.0	27164583.0	foxl2l Mut 20 2 S163 R1.fastq.gz	0:151 1:151	A:2061693689;C:2030126562;G:2072980952;T:2038873198;N:29665	151	151	2061693689	2030126562	2072980952	2038873198	29665	SRX24787625	SRS21505095	SRA1887976	Institute of Hydrobiology, Chinese Academy of Sciences\|Center for Fish Biology and Fishery Biotechnology	Institute of Hydrobiology, Chinese Academy of Sciences												B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	bulk	bulk	bulk	China	2024-06-03	Undetermined	Undetermined	Gonad	Reproductive System
32486	32486	SRR29270159	SRX24787624	SRS21505094	SRP511487	PRJNA1119569	RNA seq of zebrafish foxl2l mutant	PRJNA1119569	Other	Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.			foxl2l Het 15 2	strain:AB\|age:15\|collection date:2023 06 02\|geo loc name:China\|sex:hermaphrodite\|tissue:gonad\|BioSampleModel:Model organism or animal									foxl2l Het 15 2	E2	E2	50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	NextSeq 500	SRP511487		foxl2l_Het-15-2_S154_R1.fastq.gz foxl2l_Het-15-2_S154_R2.fastq.gz	fastq fastq	7868286860.0	26053930.0	foxl2l Het 15 2 S154 R1.fastq.gz	0:151 1:151	A:1972210357;C:1946891859;G:2008091153;T:1941064817;N:28674	151	151	1972210357	1946891859	2008091153	1941064817	28674	SRX24787624	SRS21505094	SRA1887976	Institute of Hydrobiology, Chinese Academy of Sciences\|Center for Fish Biology and Fishery Biotechnology	Institute of Hydrobiology, Chinese Academy of Sciences												B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	bulk	bulk	bulk	China	2024-06-03	Undetermined	Undetermined	Gonad	Reproductive System
32487	32487	SRR29270160	SRX24787623	SRS21505093	SRP511487	PRJNA1119569	RNA seq of zebrafish foxl2l mutant	PRJNA1119569	Other	Bulk seq of zebrafish foxl2l mutant at 15 dpf and 20 dpf. Each time point contain 3 heterozygous and 3 homozygous.			foxl2l Het 15 1	strain:AB\|age:15\|collection date:2023 06 01\|geo loc name:China\|sex:hermaphrodite\|tissue:gonad\|BioSampleModel:Model organism or animal									foxl2l Het 15 1	E1	E1	50 ng of RNA was used to prepare VAHTS RNA seq Library using Universal V6 RNA seq Library Prep Kit for Illumina Vazeme NR604 01			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	NextSeq 500	SRP511487		foxl2l_Het-15-1_S153_R1.fastq.gz foxl2l_Het-15-1_S153_R2.fastq.gz	fastq fastq	7117391946.0	23567523.0	foxl2l Het 15 1 S153 R1.fastq.gz	0:151 1:151	A:1795668098;C:1752824783;G:1793720116;T:1775153584;N:25365	151	151	1795668098	1752824783	1793720116	1775153584	25365	SRX24787623	SRS21505093	SRA1887976	Institute of Hydrobiology, Chinese Academy of Sciences\|Center for Fish Biology and Fishery Biotechnology	Institute of Hydrobiology, Chinese Academy of Sciences												B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	bulk	bulk	bulk	China	2024-06-03	Undetermined	Undetermined	Gonad	Reproductive System
34094	34094	SRR31050909	SRX26435351	SRS22952031	SRP539687	PRJNA1175381	Short term polystyrene nanoplastic exposure alters zebrafish male and female germline and reproductive outcomes unveiling pollutant impacted molecular pathways	GSE279916	Transcriptome Analysis	Nanoplastics pollution is a rising environmental concern whose impacts on biodiversity and human health are far from being understood. This is particularly salient in aquatic ecosystems where the majority of species depend on external fertilization for reproduction. Here we evaluated the effects of a short term exposure to engineered polystyrene nanoplastics NPs in the zebrafish germ line to further explore their impact on reproduction. To this end zebrafish Danio rerio were exposed to 5 mg/L of 45 nm polystyrene PS NPs via water for 96h. We show that in males nanoplastics induced testicular histological alterations with abnormal sperm clustering and chromatin compaction resulting in viable spermatozoa but with reduced motility. Moreover in females we observed an alteration in oocyte stages frequencies during oogenesis possibly reflecting alterations in oocyte growth. RNA sequencing analysis in male testis links nanoplastic induced alterations in the expression of genes involved in chromatin structure meiosis and DNA double strand break formation and repair progression and gametes recognition. Flow cytometry analysis revealed that the observed effects in males were directly due to nanoplastics penetrating the testicular barrier and being internalized within germline cells. Overall our results demonstrate that acute exposure to NPs can compromise reproductive fitness underscoring the environmental and health impacts of NPs pollution. Overall design: Bulk RNA seq from adult testis from control 3 samples and treated animals 3 samples	pubmed:39556913	Zebrafish Testicle Plastic Replicate 3 Animal 3	GSM8583344	source name:testicles\|tissue:testicles\|cell line:germline\|genotype:WT\|treatment:Plastic\|geo loc name:missing\|collection date:missing	Zebrafish Testicle Plastic Replicate 3 Animal 3	Anaconda The sequencing quality was checked before performing the assembly. STAR bioconda was used for the assembly smartools bioconda was used to generate the intermediate files Sam and Bam Counts were obtained from the bam intermediate file Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample	testicles	Half of the fish were exposed to polystyrene nanoplastics each 24 hours added in the water during 96 hours accute exposure. The rest were used as controls so no plastics were added in the water.	Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene using poly A enrichment	Adult zebrafish were maintained at the animal house under standard conditions	tissue:testicles\|cell line:germline\|genotype:WT\|treatment:Plastic	GSM8583344	GSM8583344: Zebrafish Testicle Plastic Replicate 3 Animal 3; Danio rerio; RNA Seq	GSM8583344 r1	GSM8583344	1	Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene using poly A enrichment		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP539687		M6_C2_R3_A3_EKRN230074904-1A_HWT7HDSX7_L3_1.fq M6_C2_R3_A3_EKRN230074904-1A_HWT7HDSX7_L3_2.fq	fastq fastq	24813339000.0	82711130.0	GSM8583344 r1										SRX26435351	SRS22952031	SRA1994234	UAB (Universidad Autónoma de Barcelona)	UAB (Universidad Autónoma de Barcelona)												B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	Spain	2024-10-20	Adult	Adult	Gonad	Reproductive System
34095	34095	SRR31050910	SRX26435350	SRS22952030	SRP539687	PRJNA1175381	Short term polystyrene nanoplastic exposure alters zebrafish male and female germline and reproductive outcomes unveiling pollutant impacted molecular pathways	GSE279916	Transcriptome Analysis	Nanoplastics pollution is a rising environmental concern whose impacts on biodiversity and human health are far from being understood. This is particularly salient in aquatic ecosystems where the majority of species depend on external fertilization for reproduction. Here we evaluated the effects of a short term exposure to engineered polystyrene nanoplastics NPs in the zebrafish germ line to further explore their impact on reproduction. To this end zebrafish Danio rerio were exposed to 5 mg/L of 45 nm polystyrene PS NPs via water for 96h. We show that in males nanoplastics induced testicular histological alterations with abnormal sperm clustering and chromatin compaction resulting in viable spermatozoa but with reduced motility. Moreover in females we observed an alteration in oocyte stages frequencies during oogenesis possibly reflecting alterations in oocyte growth. RNA sequencing analysis in male testis links nanoplastic induced alterations in the expression of genes involved in chromatin structure meiosis and DNA double strand break formation and repair progression and gametes recognition. Flow cytometry analysis revealed that the observed effects in males were directly due to nanoplastics penetrating the testicular barrier and being internalized within germline cells. Overall our results demonstrate that acute exposure to NPs can compromise reproductive fitness underscoring the environmental and health impacts of NPs pollution. Overall design: Bulk RNA seq from adult testis from control 3 samples and treated animals 3 samples	pubmed:39556913	Zebrafish Testicle Plastic Replicate 3 Animal 1	GSM8583343	source name:testicles\|tissue:testicles\|cell line:germline\|genotype:WT\|treatment:Plastic\|geo loc name:missing\|collection date:missing	Zebrafish Testicle Plastic Replicate 3 Animal 1	Anaconda The sequencing quality was checked before performing the assembly. STAR bioconda was used for the assembly smartools bioconda was used to generate the intermediate files Sam and Bam Counts were obtained from the bam intermediate file Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample	testicles	Half of the fish were exposed to polystyrene nanoplastics each 24 hours added in the water during 96 hours accute exposure. The rest were used as controls so no plastics were added in the water.	Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene using poly A enrichment	Adult zebrafish were maintained at the animal house under standard conditions	tissue:testicles\|cell line:germline\|genotype:WT\|treatment:Plastic	GSM8583343	GSM8583343: Zebrafish Testicle Plastic Replicate 3 Animal 1; Danio rerio; RNA Seq	GSM8583343 r1	GSM8583343	1	Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene using poly A enrichment		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP539687		M6_C2_R3_A1_EKRN230074902-1A_HWT7HDSX7_L3_1.fq M6_C2_R3_A1_EKRN230074902-1A_HWT7HDSX7_L3_2.fq	fastq fastq	21334650000.0	71115500.0	GSM8583343 r1										SRX26435350	SRS22952030	SRA1994234	UAB (Universidad Autónoma de Barcelona)	UAB (Universidad Autónoma de Barcelona)												B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	Spain	2024-10-20	Adult	Adult	Gonad	Reproductive System
34096	34096	SRR31050911	SRX26435349	SRS22952029	SRP539687	PRJNA1175381	Short term polystyrene nanoplastic exposure alters zebrafish male and female germline and reproductive outcomes unveiling pollutant impacted molecular pathways	GSE279916	Transcriptome Analysis	Nanoplastics pollution is a rising environmental concern whose impacts on biodiversity and human health are far from being understood. This is particularly salient in aquatic ecosystems where the majority of species depend on external fertilization for reproduction. Here we evaluated the effects of a short term exposure to engineered polystyrene nanoplastics NPs in the zebrafish germ line to further explore their impact on reproduction. To this end zebrafish Danio rerio were exposed to 5 mg/L of 45 nm polystyrene PS NPs via water for 96h. We show that in males nanoplastics induced testicular histological alterations with abnormal sperm clustering and chromatin compaction resulting in viable spermatozoa but with reduced motility. Moreover in females we observed an alteration in oocyte stages frequencies during oogenesis possibly reflecting alterations in oocyte growth. RNA sequencing analysis in male testis links nanoplastic induced alterations in the expression of genes involved in chromatin structure meiosis and DNA double strand break formation and repair progression and gametes recognition. Flow cytometry analysis revealed that the observed effects in males were directly due to nanoplastics penetrating the testicular barrier and being internalized within germline cells. Overall our results demonstrate that acute exposure to NPs can compromise reproductive fitness underscoring the environmental and health impacts of NPs pollution. Overall design: Bulk RNA seq from adult testis from control 3 samples and treated animals 3 samples	pubmed:39556913	Zebrafish Testicle Plastic Replicate 2 Animal 2	GSM8583342	source name:testicles\|tissue:testicles\|cell line:germline\|genotype:WT\|treatment:Plastic\|geo loc name:missing\|collection date:missing	Zebrafish Testicle Plastic Replicate 2 Animal 2	Anaconda The sequencing quality was checked before performing the assembly. STAR bioconda was used for the assembly smartools bioconda was used to generate the intermediate files Sam and Bam Counts were obtained from the bam intermediate file Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample	testicles	Half of the fish were exposed to polystyrene nanoplastics each 24 hours added in the water during 96 hours accute exposure. The rest were used as controls so no plastics were added in the water.	Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene using poly A enrichment	Adult zebrafish were maintained at the animal house under standard conditions	tissue:testicles\|cell line:germline\|genotype:WT\|treatment:Plastic	GSM8583342	GSM8583342: Zebrafish Testicle Plastic Replicate 2 Animal 2; Danio rerio; RNA Seq	GSM8583342 r1	GSM8583342	1	Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene using poly A enrichment		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP539687		M6_C2_R2_A2_EKRN230074901-1A_HWT7HDSX7_L2_1.fq M6_C2_R2_A2_EKRN230074901-1A_HWT7HDSX7_L2_2.fq	fastq fastq	23956812900.0	79856043.0	GSM8583342 r1										SRX26435349	SRS22952029	SRA1994234	UAB (Universidad Autónoma de Barcelona)	UAB (Universidad Autónoma de Barcelona)												B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	Spain	2024-10-20	Adult	Adult	Gonad	Reproductive System
34097	34097	SRR31050912	SRX26435348	SRS22952028	SRP539687	PRJNA1175381	Short term polystyrene nanoplastic exposure alters zebrafish male and female germline and reproductive outcomes unveiling pollutant impacted molecular pathways	GSE279916	Transcriptome Analysis	Nanoplastics pollution is a rising environmental concern whose impacts on biodiversity and human health are far from being understood. This is particularly salient in aquatic ecosystems where the majority of species depend on external fertilization for reproduction. Here we evaluated the effects of a short term exposure to engineered polystyrene nanoplastics NPs in the zebrafish germ line to further explore their impact on reproduction. To this end zebrafish Danio rerio were exposed to 5 mg/L of 45 nm polystyrene PS NPs via water for 96h. We show that in males nanoplastics induced testicular histological alterations with abnormal sperm clustering and chromatin compaction resulting in viable spermatozoa but with reduced motility. Moreover in females we observed an alteration in oocyte stages frequencies during oogenesis possibly reflecting alterations in oocyte growth. RNA sequencing analysis in male testis links nanoplastic induced alterations in the expression of genes involved in chromatin structure meiosis and DNA double strand break formation and repair progression and gametes recognition. Flow cytometry analysis revealed that the observed effects in males were directly due to nanoplastics penetrating the testicular barrier and being internalized within germline cells. Overall our results demonstrate that acute exposure to NPs can compromise reproductive fitness underscoring the environmental and health impacts of NPs pollution. Overall design: Bulk RNA seq from adult testis from control 3 samples and treated animals 3 samples	pubmed:39556913	Zebrafish Testicle Control Replicate 3 Animal 1	GSM8583341	source name:testicles\|tissue:testicles\|cell line:germline\|genotype:WT\|treatment:Control\|geo loc name:missing\|collection date:missing	Zebrafish Testicle Control Replicate 3 Animal 1	Anaconda The sequencing quality was checked before performing the assembly. STAR bioconda was used for the assembly smartools bioconda was used to generate the intermediate files Sam and Bam Counts were obtained from the bam intermediate file Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample	testicles	Half of the fish were exposed to polystyrene nanoplastics each 24 hours added in the water during 96 hours accute exposure. The rest were used as controls so no plastics were added in the water.	Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene using poly A enrichment	Adult zebrafish were maintained at the animal house under standard conditions	tissue:testicles\|cell line:germline\|genotype:WT\|treatment:Control	GSM8583341	GSM8583341: Zebrafish Testicle Control Replicate 3 Animal 1; Danio rerio; RNA Seq	GSM8583341 r1	GSM8583341	1	Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene using poly A enrichment		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP539687		M6_C1_R3_A1_EKRN230074898-1A_HWT7HDSX7_L2_1.fq M6_C1_R3_A1_EKRN230074898-1A_HWT7HDSX7_L2_2.fq	fastq fastq	17143802100.0	57146007.0	GSM8583341 r1	0:150 1:150	A:4588084574;C:4015807096;G:4039433882;T:4500279277;N:197271	150	150	4588084574	4015807096	4039433882	4500279277	197271	SRX26435348	SRS22952028	SRA1994234	UAB (Universidad Autónoma de Barcelona)	UAB (Universidad Autónoma de Barcelona)												B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	Spain	2024-10-20	Adult	Adult	Gonad	Reproductive System
34098	34098	SRR31050913	SRX26435347	SRS22952027	SRP539687	PRJNA1175381	Short term polystyrene nanoplastic exposure alters zebrafish male and female germline and reproductive outcomes unveiling pollutant impacted molecular pathways	GSE279916	Transcriptome Analysis	Nanoplastics pollution is a rising environmental concern whose impacts on biodiversity and human health are far from being understood. This is particularly salient in aquatic ecosystems where the majority of species depend on external fertilization for reproduction. Here we evaluated the effects of a short term exposure to engineered polystyrene nanoplastics NPs in the zebrafish germ line to further explore their impact on reproduction. To this end zebrafish Danio rerio were exposed to 5 mg/L of 45 nm polystyrene PS NPs via water for 96h. We show that in males nanoplastics induced testicular histological alterations with abnormal sperm clustering and chromatin compaction resulting in viable spermatozoa but with reduced motility. Moreover in females we observed an alteration in oocyte stages frequencies during oogenesis possibly reflecting alterations in oocyte growth. RNA sequencing analysis in male testis links nanoplastic induced alterations in the expression of genes involved in chromatin structure meiosis and DNA double strand break formation and repair progression and gametes recognition. Flow cytometry analysis revealed that the observed effects in males were directly due to nanoplastics penetrating the testicular barrier and being internalized within germline cells. Overall our results demonstrate that acute exposure to NPs can compromise reproductive fitness underscoring the environmental and health impacts of NPs pollution. Overall design: Bulk RNA seq from adult testis from control 3 samples and treated animals 3 samples	pubmed:39556913	Zebrafish Testicle Control Replicate 2 Animal 2	GSM8583340	source name:testicles\|tissue:testicles\|cell line:germline\|genotype:WT\|treatment:Control\|geo loc name:missing\|collection date:missing	Zebrafish Testicle Control Replicate 2 Animal 2	Anaconda The sequencing quality was checked before performing the assembly. STAR bioconda was used for the assembly smartools bioconda was used to generate the intermediate files Sam and Bam Counts were obtained from the bam intermediate file Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample	testicles	Half of the fish were exposed to polystyrene nanoplastics each 24 hours added in the water during 96 hours accute exposure. The rest were used as controls so no plastics were added in the water.	Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene using poly A enrichment	Adult zebrafish were maintained at the animal house under standard conditions	tissue:testicles\|cell line:germline\|genotype:WT\|treatment:Control	GSM8583340	GSM8583340: Zebrafish Testicle Control Replicate 2 Animal 2; Danio rerio; RNA Seq	GSM8583340 r1	GSM8583340	1	Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene using poly A enrichment		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP539687		M6_C1_R2_A2_1.fq M6_C1_R2_A2_2.fq	fastq fastq	17289440100.0	57631467.0	GSM8583340 r1										SRX26435347	SRS22952027	SRA1994234	UAB (Universidad Autónoma de Barcelona)	UAB (Universidad Autónoma de Barcelona)												B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	Spain	2024-10-20	Adult	Adult	Gonad	Reproductive System
34099	34099	SRR31050914	SRX26435346	SRS22952026	SRP539687	PRJNA1175381	Short term polystyrene nanoplastic exposure alters zebrafish male and female germline and reproductive outcomes unveiling pollutant impacted molecular pathways	GSE279916	Transcriptome Analysis	Nanoplastics pollution is a rising environmental concern whose impacts on biodiversity and human health are far from being understood. This is particularly salient in aquatic ecosystems where the majority of species depend on external fertilization for reproduction. Here we evaluated the effects of a short term exposure to engineered polystyrene nanoplastics NPs in the zebrafish germ line to further explore their impact on reproduction. To this end zebrafish Danio rerio were exposed to 5 mg/L of 45 nm polystyrene PS NPs via water for 96h. We show that in males nanoplastics induced testicular histological alterations with abnormal sperm clustering and chromatin compaction resulting in viable spermatozoa but with reduced motility. Moreover in females we observed an alteration in oocyte stages frequencies during oogenesis possibly reflecting alterations in oocyte growth. RNA sequencing analysis in male testis links nanoplastic induced alterations in the expression of genes involved in chromatin structure meiosis and DNA double strand break formation and repair progression and gametes recognition. Flow cytometry analysis revealed that the observed effects in males were directly due to nanoplastics penetrating the testicular barrier and being internalized within germline cells. Overall our results demonstrate that acute exposure to NPs can compromise reproductive fitness underscoring the environmental and health impacts of NPs pollution. Overall design: Bulk RNA seq from adult testis from control 3 samples and treated animals 3 samples	pubmed:39556913	Zebrafish Testicle Control Replicate 1 Animal 2	GSM8583339	source name:testicles\|tissue:testicles\|cell line:germline\|genotype:WT\|treatment:Control\|geo loc name:missing\|collection date:missing	Zebrafish Testicle Control Replicate 1 Animal 2	Anaconda The sequencing quality was checked before performing the assembly. STAR bioconda was used for the assembly smartools bioconda was used to generate the intermediate files Sam and Bam Counts were obtained from the bam intermediate file Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample	testicles	Half of the fish were exposed to polystyrene nanoplastics each 24 hours added in the water during 96 hours accute exposure. The rest were used as controls so no plastics were added in the water.	Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene using poly A enrichment	Adult zebrafish were maintained at the animal house under standard conditions	tissue:testicles\|cell line:germline\|genotype:WT\|treatment:Control	GSM8583339	GSM8583339: Zebrafish Testicle Control Replicate 1 Animal 2; Danio rerio; RNA Seq	GSM8583339 r1	GSM8583339	1	Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene using poly A enrichment		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP539687		M6_C1_R1_A2_EKRN230074896-1A_HWT7HDSX7_L2_1.fq M6_C1_R1_A2_EKRN230074896-1A_HWT7HDSX7_L2_2.fq	fastq fastq	19275937200.0	64253124.0	GSM8583339 r1	0:150 1:150	A:5148413409;C:4525316389;G:4541110001;T:5060873310;N:224091	150	150	5148413409	4525316389	4541110001	5060873310	224091	SRX26435346	SRS22952026	SRA1994234	UAB (Universidad Autónoma de Barcelona)	UAB (Universidad Autónoma de Barcelona)												B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	Spain	2024-10-20	Adult	Adult	Gonad	Reproductive System
67554	67554	SRR17210893	SRX13390812	SRS11294344	SRP350440	PRJNA788302	PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis	GSE190741	Other	The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126	pubmed:35477799	RNAseq PCB126 10nM Rep6	GSM5730194	source name:testis\|tissue:testis\|developmental stage:Adult\|treatment:PCB126 10nM	RNAseq PCB126 10nM Rep6	DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups	testis	Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.		tissue:testis\|developmental stage:Adult\|treatment:PCB126 10nM	GSM5730194	GSM5730194: RNAseq PCB126 10nM Rep6; Danio rerio; RNA Seq	GSM5730194		1	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.	GEO Accession:GSM5730194	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP350440		4170_mix-T24_S18_R1_001.fastq.gz	fastq	1912515249.0	37500299.0	GSM5730194 r1	0:51 1:0	A:477251176;C:466929755;G:439380761;T:528825431;N:128126	51	0	477251176	466929755	439380761	528825431	128126	SRX13390812	SRS11294344	SRA1342092	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.95015		0.10454		0.64922		0.53267		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-12-12	Adult	Adult	Gonad	Reproductive System
67555	67555	SRR17210892	SRX13390811	SRS11294345	SRP350440	PRJNA788302	PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis	GSE190741	Other	The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126	pubmed:35477799	RNAseq PCB126 10nM Rep5	GSM5730193	source name:testis\|tissue:testis\|developmental stage:Adult\|treatment:PCB126 10nM	RNAseq PCB126 10nM Rep5	DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups	testis	Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.		tissue:testis\|developmental stage:Adult\|treatment:PCB126 10nM	GSM5730193	GSM5730193: RNAseq PCB126 10nM Rep5; Danio rerio; RNA Seq	GSM5730193		1	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.	GEO Accession:GSM5730193	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP350440		4170_mix-T23_S17_R1_001.fastq.gz	fastq	1344965778.0	26371878.0	GSM5730193 r1	0:51 1:0	A:347349418;C:318051347;G:301879882;T:377595413;N:89718	51	0	347349418	318051347	301879882	377595413	89718	SRX13390811	SRS11294345	SRA1342092	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.94726		0.10386		0.64948		0.5434		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-12-12	Adult	Adult	Gonad	Reproductive System
67556	67556	SRR17210891	SRX13390810	SRS11294343	SRP350440	PRJNA788302	PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis	GSE190741	Other	The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126	pubmed:35477799	RNAseq PCB126 10nM Rep4	GSM5730192	source name:testis\|tissue:testis\|developmental stage:Adult\|treatment:PCB126 10nM	RNAseq PCB126 10nM Rep4	DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups	testis	Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.		tissue:testis\|developmental stage:Adult\|treatment:PCB126 10nM	GSM5730192	GSM5730192: RNAseq PCB126 10nM Rep4; Danio rerio; RNA Seq	GSM5730192		1	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.	GEO Accession:GSM5730192	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP350440		4170_mix-T21_S16_R1_001.fastq.gz	fastq	2077575474.0	40736774.0	GSM5730192 r1	0:51 1:0	A:507322408;C:503941476;G:510925051;T:555250063;N:136476	51	0	507322408	503941476	510925051	555250063	136476	SRX13390810	SRS11294343	SRA1342092	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.95021		0.06976		0.6464		0.50296		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-12-12	Adult	Adult	Gonad	Reproductive System
67557	67557	SRR17210890	SRX13390809	SRS11294342	SRP350440	PRJNA788302	PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis	GSE190741	Other	The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126	pubmed:35477799	RNAseq PCB126 10nM Rep3	GSM5730191	source name:testis\|tissue:testis\|developmental stage:Adult\|treatment:PCB126 10nM	RNAseq PCB126 10nM Rep3	DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups	testis	Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.		tissue:testis\|developmental stage:Adult\|treatment:PCB126 10nM	GSM5730191	GSM5730191: RNAseq PCB126 10nM Rep3; Danio rerio; RNA Seq	GSM5730191		1	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.	GEO Accession:GSM5730191	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP350440		4170_mix-T19_S15_R1_001.fastq.gz	fastq	1514204127.0	29690277.0	GSM5730191 r1	0:51 1:0	A:362659383;C:370554761;G:356314539;T:424574865;N:100579	51	0	362659383	370554761	356314539	424574865	100579	SRX13390809	SRS11294342	SRA1342092	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.95191		0.07368		0.62509		0.48965		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-12-12	Adult	Adult	Gonad	Reproductive System
67558	67558	SRR17210889	SRX13390808	SRS11294341	SRP350440	PRJNA788302	PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis	GSE190741	Other	The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126	pubmed:35477799	RNAseq PCB126 10nM Rep2	GSM5730190	source name:testis\|tissue:testis\|developmental stage:Adult\|treatment:PCB126 10nM	RNAseq PCB126 10nM Rep2	DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups	testis	Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.		tissue:testis\|developmental stage:Adult\|treatment:PCB126 10nM	GSM5730190	GSM5730190: RNAseq PCB126 10nM Rep2; Danio rerio; RNA Seq	GSM5730190		1	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.	GEO Accession:GSM5730190	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP350440		4170_mix-T18_S14_R1_001.fastq.gz	fastq	1381687155.0	27091905.0	GSM5730190 r1	0:51 1:0	A:333912162;C:335458932;G:326378401;T:385845588;N:92072	51	0	333912162	335458932	326378401	385845588	92072	SRX13390808	SRS11294341	SRA1342092	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.95313		0.07433		0.63177		0.50475		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-12-12	Adult	Adult	Gonad	Reproductive System
67559	67559	SRR17210888	SRX13390807	SRS11294340	SRP350440	PRJNA788302	PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis	GSE190741	Other	The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126	pubmed:35477799	RNAseq PCB126 10nM Rep1	GSM5730189	source name:testis\|tissue:testis\|developmental stage:Adult\|treatment:PCB126 10nM	RNAseq PCB126 10nM Rep1	DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups	testis	Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.		tissue:testis\|developmental stage:Adult\|treatment:PCB126 10nM	GSM5730189	GSM5730189: RNAseq PCB126 10nM Rep1; Danio rerio; RNA Seq	GSM5730189		1	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.	GEO Accession:GSM5730189	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP350440		4170_mix-T17_S13_R1_001.fastq.gz	fastq	1508524920.0	29578920.0	GSM5730189 r1	0:51 1:0	A:393426431;C:349348415;G:337538750;T:428110887;N:100437	51	0	393426431	349348415	337538750	428110887	100437	SRX13390807	SRS11294340	SRA1342092	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.94765		0.0935		0.64743		0.53646		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-12-12	Adult	Adult	Gonad	Reproductive System
67560	67560	SRR17210887	SRX13390806	SRS11294338	SRP350440	PRJNA788302	PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis	GSE190741	Other	The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126	pubmed:35477799	RNAseq PCB126 3nM Rep6	GSM5730188	source name:testis\|tissue:testis\|developmental stage:Adult\|treatment:PCB126 3nM	RNAseq PCB126 3nM Rep6	DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups	testis	Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.		tissue:testis\|developmental stage:Adult\|treatment:PCB126 3nM	GSM5730188	GSM5730188: RNAseq PCB126 3nM Rep6; Danio rerio; RNA Seq	GSM5730188		1	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.	GEO Accession:GSM5730188	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP350440		4170_mix-T16_S12_R1_001.fastq.gz	fastq	1840726935.0	36092685.0	GSM5730188 r1	0:51 1:0	A:466997928;C:437493060;G:421124744;T:514986449;N:124754	51	0	466997928	437493060	421124744	514986449	124754	SRX13390806	SRS11294338	SRA1342092	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.9474		0.0984		0.64165		0.51348		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-12-12	Adult	Adult	Gonad	Reproductive System
67561	67561	SRR17210886	SRX13390805	SRS11294339	SRP350440	PRJNA788302	PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis	GSE190741	Other	The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126	pubmed:35477799	RNAseq PCB126 3nM Rep5	GSM5730187	source name:testis\|tissue:testis\|developmental stage:Adult\|treatment:PCB126 3nM	RNAseq PCB126 3nM Rep5	DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups	testis	Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.		tissue:testis\|developmental stage:Adult\|treatment:PCB126 3nM	GSM5730187	GSM5730187: RNAseq PCB126 3nM Rep5; Danio rerio; RNA Seq	GSM5730187		1	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.	GEO Accession:GSM5730187	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP350440		4170_mix-T15_S11_R1_001.fastq.gz	fastq	1384282545.0	27142795.0	GSM5730187 r1	0:51 1:0	A:325552702;C:343473865;G:329054590;T:386110707;N:90681	51	0	325552702	343473865	329054590	386110707	90681	SRX13390805	SRS11294339	SRA1342092	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.95623		0.06621		0.63345		0.49688		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-12-12	Adult	Adult	Gonad	Reproductive System
67562	67562	SRR17210885	SRX13390804	SRS11294337	SRP350440	PRJNA788302	PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis	GSE190741	Other	The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126	pubmed:35477799	RNAseq PCB126 3nM Rep4	GSM5730186	source name:testis\|tissue:testis\|developmental stage:Adult\|treatment:PCB126 3nM	RNAseq PCB126 3nM Rep4	DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups	testis	Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.		tissue:testis\|developmental stage:Adult\|treatment:PCB126 3nM	GSM5730186	GSM5730186: RNAseq PCB126 3nM Rep4; Danio rerio; RNA Seq	GSM5730186		1	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.	GEO Accession:GSM5730186	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP350440		4170_mix-T14_S10_R1_001.fastq.gz	fastq	2099071260.0	41158260.0	GSM5730186 r1	0:51 1:0	A:525168723;C:513155313;G:482406202;T:578202593;N:138429	51	0	525168723	513155313	482406202	578202593	138429	SRX13390804	SRS11294337	SRA1342092	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.94639		0.10285		0.64942		0.50757		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-12-12	Adult	Adult	Gonad	Reproductive System
67563	67563	SRR17210884	SRX13390803	SRS11294336	SRP350440	PRJNA788302	PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis	GSE190741	Other	The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126	pubmed:35477799	RNAseq PCB126 3nM Rep3	GSM5730185	source name:testis\|tissue:testis\|developmental stage:Adult\|treatment:PCB126 3nM	RNAseq PCB126 3nM Rep3	DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups	testis	Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.		tissue:testis\|developmental stage:Adult\|treatment:PCB126 3nM	GSM5730185	GSM5730185: RNAseq PCB126 3nM Rep3; Danio rerio; RNA Seq	GSM5730185		1	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.	GEO Accession:GSM5730185	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP350440		4170_mix-T13_S9_R1_001.fastq.gz	fastq	1877300055.0	36809805.0	GSM5730185 r1	0:51 1:0	A:447373671;C:463401185;G:439915337;T:526483226;N:126636	51	0	447373671	463401185	439915337	526483226	126636	SRX13390803	SRS11294336	SRA1342092	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.95301		0.06979		0.64319		0.49994		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-12-12	Adult	Adult	Gonad	Reproductive System
67564	67564	SRR17210883	SRX13390802	SRS11294335	SRP350440	PRJNA788302	PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis	GSE190741	Other	The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126	pubmed:35477799	RNAseq PCB126 3nM Rep2	GSM5730184	source name:testis\|tissue:testis\|developmental stage:Adult\|treatment:PCB126 3nM	RNAseq PCB126 3nM Rep2	DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups	testis	Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.		tissue:testis\|developmental stage:Adult\|treatment:PCB126 3nM	GSM5730184	GSM5730184: RNAseq PCB126 3nM Rep2; Danio rerio; RNA Seq	GSM5730184		1	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.	GEO Accession:GSM5730184	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP350440		4170_mix-T11_S8_R1_001.fastq.gz	fastq	1788165621.0	35062071.0	GSM5730184 r1	0:51 1:0	A:420221044;C:445407082;G:423493165;T:498924231;N:120099	51	0	420221044	445407082	423493165	498924231	120099	SRX13390802	SRS11294335	SRA1342092	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.95488		0.06451		0.63126		0.49662		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-12-12	Adult	Adult	Gonad	Reproductive System
67565	67565	SRR17210882	SRX13390801	SRS11294334	SRP350440	PRJNA788302	PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis	GSE190741	Other	The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126	pubmed:35477799	RNAseq PCB126 3nM Rep1	GSM5730183	source name:testis\|tissue:testis\|developmental stage:Adult\|treatment:PCB126 3nM	RNAseq PCB126 3nM Rep1	DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups	testis	Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.		tissue:testis\|developmental stage:Adult\|treatment:PCB126 3nM	GSM5730183	GSM5730183: RNAseq PCB126 3nM Rep1; Danio rerio; RNA Seq	GSM5730183		1	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.	GEO Accession:GSM5730183	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP350440		4170_mix-T9_S7_R1_001.fastq.gz	fastq	1855410702.0	36380602.0	GSM5730183 r1	0:51 1:0	A:459292963;C:465999847;G:421852734;T:508143917;N:121241	51	0	459292963	465999847	421852734	508143917	121241	SRX13390801	SRS11294334	SRA1342092	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.95181		0.07794		0.65141		0.51342		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-12-12	Adult	Adult	Gonad	Reproductive System
67566	67566	SRR17210881	SRX13390800	SRS11294333	SRP350440	PRJNA788302	PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis	GSE190741	Other	The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126	pubmed:35477799	RNAseq DMSO Rep6	GSM5730182	source name:testis\|tissue:testis\|developmental stage:Adult\|treatment:DMSO	RNAseq DMSO Rep6	DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups	testis	Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.		tissue:testis\|developmental stage:Adult\|treatment:DMSO	GSM5730182	GSM5730182: RNAseq DMSO Rep6; Danio rerio; RNA Seq	GSM5730182		1	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.	GEO Accession:GSM5730182	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP350440		4170_mix-T8_S6_R1_001.fastq.gz	fastq	1923223464.0	37710264.0	GSM5730182 r1	0:51 1:0	A:451684628;C:481126641;G:454781274;T:535502647;N:128274	51	0	451684628	481126641	454781274	535502647	128274	SRX13390800	SRS11294333	SRA1342092	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.95508		0.07375		0.63183		0.49887		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-12-12	Adult	Adult	Gonad	Reproductive System
67567	67567	SRR17210880	SRX13390799	SRS11294332	SRP350440	PRJNA788302	PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis	GSE190741	Other	The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126	pubmed:35477799	RNAseq DMSO Rep5	GSM5730181	source name:testis\|tissue:testis\|developmental stage:Adult\|treatment:DMSO	RNAseq DMSO Rep5	DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups	testis	Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.		tissue:testis\|developmental stage:Adult\|treatment:DMSO	GSM5730181	GSM5730181: RNAseq DMSO Rep5; Danio rerio; RNA Seq	GSM5730181		1	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.	GEO Accession:GSM5730181	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP350440		4170_mix-T6_S5_R1_001.fastq.gz	fastq	1752584247.0	34364397.0	GSM5730181 r1	0:51 1:0	A:413763719;C:434326065;G:412787803;T:491589762;N:116898	51	0	413763719	434326065	412787803	491589762	116898	SRX13390799	SRS11294332	SRA1342092	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.95515		0.06656		0.63859		0.49877		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-12-12	Adult	Adult	Gonad	Reproductive System
67568	67568	SRR17210879	SRX13390798	SRS11294331	SRP350440	PRJNA788302	PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis	GSE190741	Other	The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126	pubmed:35477799	RNAseq DMSO Rep4	GSM5730180	source name:testis\|tissue:testis\|developmental stage:Adult\|treatment:DMSO	RNAseq DMSO Rep4	DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups	testis	Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.		tissue:testis\|developmental stage:Adult\|treatment:DMSO	GSM5730180	GSM5730180: RNAseq DMSO Rep4; Danio rerio; RNA Seq	GSM5730180		1	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.	GEO Accession:GSM5730180	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP350440		4170_mix-T5_S4_R1_001.fastq.gz	fastq	1783559199.0	34971749.0	GSM5730180 r1	0:51 1:0	A:426389805;C:442827488;G:416807133;T:497417118;N:117655	51	0	426389805	442827488	416807133	497417118	117655	SRX13390798	SRS11294331	SRA1342092	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.95322		0.0736		0.6354		0.49805		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-12-12	Adult	Adult	Gonad	Reproductive System
67569	67569	SRR17210878	SRX13390797	SRS11294329	SRP350440	PRJNA788302	PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis	GSE190741	Other	The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126	pubmed:35477799	RNAseq DMSO Rep3	GSM5730179	source name:testis\|tissue:testis\|developmental stage:Adult\|treatment:DMSO	RNAseq DMSO Rep3	DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups	testis	Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.		tissue:testis\|developmental stage:Adult\|treatment:DMSO	GSM5730179	GSM5730179: RNAseq DMSO Rep3; Danio rerio; RNA Seq	GSM5730179		1	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.	GEO Accession:GSM5730179	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP350440		4170_mix-T4_S3_R1_001.fastq.gz	fastq	1907367207.0	37399357.0	GSM5730179 r1	0:51 1:0	A:508707164;C:436434670;G:414734236;T:547363631;N:127506	51	0	508707164	436434670	414734236	547363631	127506	SRX13390797	SRS11294329	SRA1342092	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.50915		0.03593		0.70147		0.49838		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-12-12	Adult	Adult	Gonad	Reproductive System
67570	67570	SRR17210877	SRX13390796	SRS11294330	SRP350440	PRJNA788302	PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis	GSE190741	Other	The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126	pubmed:35477799	RNAseq DMSO Rep2	GSM5730178	source name:testis\|tissue:testis\|developmental stage:Adult\|treatment:DMSO	RNAseq DMSO Rep2	DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups	testis	Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.		tissue:testis\|developmental stage:Adult\|treatment:DMSO	GSM5730178	GSM5730178: RNAseq DMSO Rep2; Danio rerio; RNA Seq	GSM5730178		1	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.	GEO Accession:GSM5730178	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP350440		4170_mix-T3_S2_R1_001.fastq.gz	fastq	1756085856.0	34433056.0	GSM5730178 r1	0:51 1:0	A:409690032;C:438746739;G:419437935;T:488094432;N:116718	51	0	409690032	438746739	419437935	488094432	116718	SRX13390796	SRS11294330	SRA1342092	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.95577		0.06639		0.64076		0.49674		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-12-12	Adult	Adult	Gonad	Reproductive System
67571	67571	SRR17210876	SRX13390795	SRS11294328	SRP350440	PRJNA788302	PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis	GSE190741	Other	The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3 three prime 4 4' 5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized involving activation of aryl hydrocarbon receptor a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing nucleoside metabolic process iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control 3nM PCB126 and 10 nM PCB126	pubmed:35477799	RNAseq DMSO Rep1	GSM5730177	source name:testis\|tissue:testis\|developmental stage:Adult\|treatment:DMSO	RNAseq DMSO Rep1	DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules Mapping Calling Analysis and DMRs RNAseq pre processing using FASTQC RNAseq mapping the reads to the genome using STAR RNAseq counting the reads using HT seq count RNAseq statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups	testis	Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.		tissue:testis\|developmental stage:Adult\|treatment:DMSO	GSM5730177	GSM5730177: RNAseq DMSO Rep1; Danio rerio; RNA Seq	GSM5730177		1	Total RNA and DNA were isolated using the ZR Duet™ DNA/RNA Mini Prep kit Zymo Research CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50 bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx a Diagenode company Ghent Belgium. Briefly libraries were prepared from 500 ng of genomic DNA digested with 30 units of MspI New England Biolabs MA followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.	GEO Accession:GSM5730177	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP350440		4170_mix-T1_S1_R1_001.fastq.gz	fastq	1791620310.0	35129810.0	GSM5730177 r1	0:51 1:0	A:422311870;C:442811083;G:428686648;T:497691822;N:118887	51	0	422311870	442811083	428686648	497691822	118887	SRX13390795	SRS11294328	SRA1342092	GEO	Aluru Lab, Biology, Woods Hole Oceanographic Institution	1	0.95683		0.06919		0.6495		0.49403		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2021-12-12	Adult	Adult	Gonad	Reproductive 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");;