metadata: run_metadata: 26 rows where experiment.library_layout = "SINGLE", technology = "bulk" and tissue_curation

26 rows where experiment.library_layout = "SINGLE", technology = "bulk" and tissue_curation_coarse = "Reproductive System"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
30755	30755	SRR28348921	SRX23954975	SRS20755396	SRP495323	PRJNA1088158	Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.	GSE261646	Transcriptome Analysis	The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…	pubmed:39302832	Zebrafish Oocyte Stage IV rep2	GSM8147872	source name:Oocyte\|tissue:Oocyte\|developmental stage:Stage IV\|genotype:AB TF and TLF\|geo loc name:missing\|collection date:missing	Zebrafish Oocyte Stage IV rep2	Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates	Oocyte		Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.	tissue:Oocyte\|developmental stage:Stage IV\|genotype:AB TF and TLF	GSM8147872	GSM8147872: Zebrafish Oocyte Stage IV rep2; Danio rerio; RNA Seq	GSM8147872 r1	GSM8147872	1	Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP495323	Z_oocyte_stage_4_2_Pa.fastq	fastq	2456514332.0	32322557.0	GSM8147872 r1	0:76	A:588246161;C:609187233;G:593122683;T:665837765;N:120490	76		588246161	609187233	593122683	665837765	120490	SRX23954975	SRS20755396	SRA1824599	Computational Biology, Stowers Institute for Medical Research	Computational Biology, Stowers Institute for Medical Research							B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2024-03-14	Multi-stage	Embryo	Oocyte	Reproductive System
30756	30756	SRR28348922	SRX23954974	SRS20755395	SRP495323	PRJNA1088158	Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.	GSE261646	Transcriptome Analysis	The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…	pubmed:39302832	Zebrafish Oocyte Stage IV rep1	GSM8147871	source name:Oocyte\|tissue:Oocyte\|developmental stage:Stage IV\|genotype:AB TF and TLF\|geo loc name:missing\|collection date:missing	Zebrafish Oocyte Stage IV rep1	Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates	Oocyte		Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.	tissue:Oocyte\|developmental stage:Stage IV\|genotype:AB TF and TLF	GSM8147871	GSM8147871: Zebrafish Oocyte Stage IV rep1; Danio rerio; RNA Seq	GSM8147871 r1	GSM8147871	1	Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP495323	Z_oocyte_stage_4_1_Pa.fastq	fastq	2650784696.0	34878746.0	GSM8147871 r1	0:76	A:649971632;C:640667370;G:632570967;T:727447552;N:127175	76		649971632	640667370	632570967	727447552	127175	SRX23954974	SRS20755395	SRA1824599	Computational Biology, Stowers Institute for Medical Research	Computational Biology, Stowers Institute for Medical Research							B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2024-03-14	Multi-stage	Embryo	Oocyte	Reproductive System
30757	30757	SRR28348923	SRX23954973	SRS20755394	SRP495323	PRJNA1088158	Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.	GSE261646	Transcriptome Analysis	The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…	pubmed:39302832	Zebrafish Oocyte Stage III rep2	GSM8147870	source name:Oocyte\|tissue:Oocyte\|developmental stage:Stage III\|genotype:AB TF and TLF\|geo loc name:missing\|collection date:missing	Zebrafish Oocyte Stage III rep2	Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates	Oocyte		Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.	tissue:Oocyte\|developmental stage:Stage III\|genotype:AB TF and TLF	GSM8147870	GSM8147870: Zebrafish Oocyte Stage III rep2; Danio rerio; RNA Seq	GSM8147870 r1	GSM8147870	1	Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP495323	Z_oocyte_stage_3_2_Pa.fastq	fastq	2809957956.0	36973131.0	GSM8147870 r1	0:76	A:679041537;C:690924547;G:702857353;T:736996218;N:138301	76		679041537	690924547	702857353	736996218	138301	SRX23954973	SRS20755394	SRA1824599	Computational Biology, Stowers Institute for Medical Research	Computational Biology, Stowers Institute for Medical Research							B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2024-03-14	Multi-stage	Embryo	Oocyte	Reproductive System
30758	30758	SRR28348924	SRX23954972	SRS20755393	SRP495323	PRJNA1088158	Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.	GSE261646	Transcriptome Analysis	The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…	pubmed:39302832	Zebrafish Oocyte Stage III rep1	GSM8147869	source name:Oocyte\|tissue:Oocyte\|developmental stage:Stage III\|genotype:AB TF and TLF\|geo loc name:missing\|collection date:missing	Zebrafish Oocyte Stage III rep1	Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates	Oocyte		Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.	tissue:Oocyte\|developmental stage:Stage III\|genotype:AB TF and TLF	GSM8147869	GSM8147869: Zebrafish Oocyte Stage III rep1; Danio rerio; RNA Seq	GSM8147869 r1	GSM8147869	1	Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP495323	Z_oocyte_stage_3_1_Pa.fastq	fastq	2828372376.0	37215426.0	GSM8147869 r1	0:76	A:701751055;C:680571938;G:664212213;T:781698241;N:138929	76		701751055	680571938	664212213	781698241	138929	SRX23954972	SRS20755393	SRA1824599	Computational Biology, Stowers Institute for Medical Research	Computational Biology, Stowers Institute for Medical Research							B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2024-03-14	Multi-stage	Embryo	Oocyte	Reproductive System
30759	30759	SRR28348925	SRX23954971	SRS20755392	SRP495323	PRJNA1088158	Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.	GSE261646	Transcriptome Analysis	The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…	pubmed:39302832	Zebrafish Oocyte Stage II rep2	GSM8147868	source name:Oocyte\|tissue:Oocyte\|developmental stage:Stage II\|genotype:AB TF and TLF\|geo loc name:missing\|collection date:missing	Zebrafish Oocyte Stage II rep2	Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates	Oocyte		Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.	tissue:Oocyte\|developmental stage:Stage II\|genotype:AB TF and TLF	GSM8147868	GSM8147868: Zebrafish Oocyte Stage II rep2; Danio rerio; RNA Seq	GSM8147868 r1	GSM8147868	1	Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP495323	Z_oocyte_stage_2_2_Pa.fastq	fastq	2837652432.0	37337532.0	GSM8147868 r1	0:76	A:698931608;C:681467909;G:683751172;T:773364392;N:137351	76		698931608	681467909	683751172	773364392	137351	SRX23954971	SRS20755392	SRA1824599	Computational Biology, Stowers Institute for Medical Research	Computational Biology, Stowers Institute for Medical Research							B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2024-03-14	Multi-stage	Embryo	Oocyte	Reproductive System
30760	30760	SRR28348926	SRX23954970	SRS20755391	SRP495323	PRJNA1088158	Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.	GSE261646	Transcriptome Analysis	The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…	pubmed:39302832	Zebrafish Oocyte Stage II rep1	GSM8147867	source name:Oocyte\|tissue:Oocyte\|developmental stage:Stage II\|genotype:AB TF and TLF\|geo loc name:missing\|collection date:missing	Zebrafish Oocyte Stage II rep1	Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates	Oocyte		Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.	tissue:Oocyte\|developmental stage:Stage II\|genotype:AB TF and TLF	GSM8147867	GSM8147867: Zebrafish Oocyte Stage II rep1; Danio rerio; RNA Seq	GSM8147867 r1	GSM8147867	1	Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP495323	Z_oocyte_stage_2_1_Pa.fastq	fastq	3360126820.0	44212195.0	GSM8147867 r1	0:76	A:829333798;C:802089215;G:804982077;T:923557236;N:164494	76		829333798	802089215	804982077	923557236	164494	SRX23954970	SRS20755391	SRA1824599	Computational Biology, Stowers Institute for Medical Research	Computational Biology, Stowers Institute for Medical Research							B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2024-03-14	Multi-stage	Embryo	Oocyte	Reproductive System
30761	30761	SRR28348927	SRX23954969	SRS20755390	SRP495323	PRJNA1088158	Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.	GSE261646	Transcriptome Analysis	The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…	pubmed:39302832	Zebrafish Oocyte Stage I rep2	GSM8147866	source name:Oocyte\|tissue:Oocyte\|developmental stage:Stage I\|genotype:AB TF and TLF\|geo loc name:missing\|collection date:missing	Zebrafish Oocyte Stage I rep2	Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates	Oocyte		Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.	tissue:Oocyte\|developmental stage:Stage I\|genotype:AB TF and TLF	GSM8147866	GSM8147866: Zebrafish Oocyte Stage I rep2; Danio rerio; RNA Seq	GSM8147866 r1	GSM8147866	1	Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP495323	Z_oocyte_stage_1_2_Pa.fastq	fastq	2739674220.0	36048345.0	GSM8147866 r1	0:76	A:653441701;C:681445567;G:663740568;T:740918288;N:128096	76		653441701	681445567	663740568	740918288	128096	SRX23954969	SRS20755390	SRA1824599	Computational Biology, Stowers Institute for Medical Research	Computational Biology, Stowers Institute for Medical Research							B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2024-03-14	Multi-stage	Embryo	Oocyte	Reproductive System
30762	30762	SRR28348928	SRX23954968	SRS20755389	SRP495323	PRJNA1088158	Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.	GSE261646	Transcriptome Analysis	The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…	pubmed:39302832	Zebrafish Oocyte Stage I rep1	GSM8147865	source name:Oocyte\|tissue:Oocyte\|developmental stage:Stage I\|genotype:AB TF and TLF\|geo loc name:missing\|collection date:missing	Zebrafish Oocyte Stage I rep1	Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates	Oocyte		Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.	tissue:Oocyte\|developmental stage:Stage I\|genotype:AB TF and TLF	GSM8147865	GSM8147865: Zebrafish Oocyte Stage I rep1; Danio rerio; RNA Seq	GSM8147865 r1	GSM8147865	1	Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP495323	Z_oocyte_stage_1_1_Pa.fastq	fastq	3348831852.0	44063577.0	GSM8147865 r1	0:76	A:815134657;C:817210346;G:809175239;T:907149915;N:161695	76		815134657	817210346	809175239	907149915	161695	SRX23954968	SRS20755389	SRA1824599	Computational Biology, Stowers Institute for Medical Research	Computational Biology, Stowers Institute for Medical Research							B	usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2024-03-14	Multi-stage	Embryo	Oocyte	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

Advanced export

JSON shape: default, array, newline-delimited

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");;