metadata: run_metadata: 201 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "cDNA" and tissue_curation

201 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "cDNA" 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.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.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
50	50	DRR029944	DRX026962	DRS086502	DRP004756	PRJDB3475	Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004756	Other	To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.			ovulation duirng natural paring	zebrafish ovary isolated from adult fish at ovulation duirng natural paring. [RNAseq]	SAMD00025434		sample name:6 Ovu\|strain:roy\|tissue type:ovary\|dev stage:adult									Illumina HiSeq 2500 sequencing of SAMD00025434	DRX026962	6 Ovu	1	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP004756	Illumina HiSeq 2500 sequencing of SAMD00025434				351766656.0	9771296.0	DRR029944	0:36	A:79811727;C:85391142;G:90185809;T:96371771;N:6207	36		79811727	85391142	90185809	96371771	6207	DRX026962	DRS086502	DRA003031	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.91956	0.01686	0.76637	0.45997	36	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
52	52	DRR029942	DRX026960	DRS086500	DRP004756	PRJDB3475	Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004756	Other	To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.			in vivo testosterone treatment	zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq replicate]	SAMD00025432		sample name:4 Tes rep\|strain:roy\|tissue type:ovary\|dev stage:adult									Illumina HiSeq 2500 sequencing of SAMD00025432	DRX026960	4 Tes rep	1	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP004756	Illumina HiSeq 2500 sequencing of SAMD00025432				366042528.0	10167848.0	DRR029942	0:36	A:84988522;C:88640326;G:93559022;T:98847003;N:7655	36		84988522	88640326	93559022	98847003	7655	DRX026960	DRS086500	DRA003031	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.91602	0.01846	0.76015	0.46475	36	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
53	53	DRR029941	DRX026959	DRS086499	DRP004756	PRJDB3475	Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004756	Other	To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.			in vivo testosterone treatment	zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq]	SAMD00025431		sample name:4 Tes\|strain:roy\|tissue type:ovary\|dev stage:adult									Illumina HiSeq 2500 sequencing of SAMD00025431	DRX026959	4 Tes	1	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP004756	Illumina HiSeq 2500 sequencing of SAMD00025431				1269835992.0	35273222.0	DRR029941	0:36	A:275250658;C:323605136;G:316729009;T:354204170;N:47019	36		275250658	323605136	316729009	354204170	47019	DRX026959	DRS086499	DRA003031	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.91467	0.02353	0.75962	0.46861	36	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
54	54	DRR029940	DRX026958	DRS086498	DRP004756	PRJDB3475	Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004756	Other	To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.			in vivo diethylstilbestrol DES treatment	zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq replicate]	SAMD00025430		sample name:3 DES rep\|strain:roy\|tissue type:ovary\|dev stage:adult									Illumina HiSeq 2500 sequencing of SAMD00025430	DRX026958	3 DES rep	1	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP004756	Illumina HiSeq 2500 sequencing of SAMD00025430				658651536.0	18295876.0	DRR029940										DRX026958	DRS086498	DRA003031	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.89964	0.01785	0.76451	0.45872	36	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
55	55	DRR029939	DRX026957	DRS086497	DRP004756	PRJDB3475	Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004756	Other	To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.			in vivo diethylstilbestrol DES treatment	zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq]	SAMD00025429		sample name:3 DES\|strain:roy\|tissue type:ovary\|dev stage:adult									Illumina HiSeq 2500 sequencing of SAMD00025429	DRX026957	3 DES	1	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP004756	Illumina HiSeq 2500 sequencing of SAMD00025429				1202024016.0	33389556.0	DRR029939	0:36	A:263319430;C:305852921;G:298798093;T:334008544;N:45028	36		263319430	305852921	298798093	334008544	45028	DRX026957	DRS086497	DRA003031	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.90643	0.02337	0.75008	0.47587	36	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
56	56	DRR029938	DRX026956	DRS086496	DRP004756	PRJDB3475	Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004756	Other	To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.			in vivo maturation inducing hormone DHP treatment	zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq replicate]	SAMD00025428		sample name:2 DHP rep\|strain:roy\|tissue type:ovary\|dev stage:adult									Illumina HiSeq 2500 sequencing of SAMD00025428	DRX026956	2 DHP rep	1	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP004756	Illumina HiSeq 2500 sequencing of SAMD00025428				434243088.0	12062308.0	DRR029938	0:36	A:99859342;C:105890785;G:110526688;T:117957580;N:8693	36		99859342	105890785	110526688	117957580	8693	DRX026956	DRS086496	DRA003031	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.91529	0.02061	0.7595	0.45809	36	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
57	57	DRR029937	DRX026955	DRS086495	DRP004756	PRJDB3475	Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004756	Other	To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.			in vivo maturation inducing hormone DHP treatment	zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq]	SAMD00025427		sample name:2 DHP\|strain:roy\|tissue type:ovary\|dev stage:adult									Illumina HiSeq 2500 sequencing of SAMD00025427	DRX026955	2 DHP	1	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP004756	Illumina HiSeq 2500 sequencing of SAMD00025427				1463868972.0	40663027.0	DRR029937	0:36	A:316060780;C:369221844;G:372845502;T:405685804;N:55042	36		316060780	369221844	372845502	405685804	55042	DRX026955	DRS086495	DRA003031	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.91556	0.01967	0.76621	0.46541	36	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
58	58	DRR029936	DRX026954	DRS086494	DRP004756	PRJDB3475	Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004756	Other	To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.			in vivo ethanol treatment	zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq replicate]	SAMD00025426		sample name:1 EtOH rep\|strain:roy\|tissue type:ovary\|dev stage:adult									Illumina HiSeq 2500 sequencing of SAMD00025426	DRX026954	1 EtOH rep	1	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP004756	Illumina HiSeq 2500 sequencing of SAMD00025426				438020208.0	12167228.0	DRR029936	0:36	A:101672612;C:105602774;G:110120652;T:120615069;N:9101	36		101672612	105602774	110120652	120615069	9101	DRX026954	DRS086494	DRA003031	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.90777	0.01929	0.7652	0.45988	36	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
59	59	DRR029935	DRX026953	DRS086493	DRP004756	PRJDB3475	Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004756	Other	To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.			in vivo ethanol treatment	zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq]	SAMD00025425		sample name:1 EtOH\|strain:roy\|tissue type:ovary\|dev stage:adult									Illumina HiSeq 2500 sequencing of SAMD00025425	DRX026953	1 EtOH	1	1		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP004756	Illumina HiSeq 2500 sequencing of SAMD00025425				1365603372.0	37933427.0	DRR029935	0:36	A:299786286;C:345487829;G:342408447;T:377870789;N:50021	36		299786286	345487829	342408447	377870789	50021	DRX026953	DRS086493	DRA003031	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.91103	0.02142	0.75402	0.46574	36	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
15550	15550	ERR647595	ERX604031	ERS557915	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.				Egg	SAMEA2796300	UNIVERSITY OF AMSTERDAM	Alias:Egg\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:29:23Z\|INSDC status:public\|SRA accession:ERS557915\|Sample Name:ERS557915\|Title:Zebrafish Egg samples\|dev stage:Oocytes									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:25:29:391 1	RID0024	1			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0024_016.fastq.gz	fastq	6684767188.0	89052017.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:25:29:391 1	0:75.07	A:1523328157;C:1795624453;G:1849675240;T:1516139338;N:0	75		1523328157	1795624453	1849675240	1516139338	0	ERX604031	ERS557915	ERA363845	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.89536	0.15322	0.91421	0.69019	73	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Zygote	Embryo	Oocyte	Reproductive System
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
34965	34965	SRR32588722	SRX27895229	SRS24266229	SRP568323	PRJNA1232602	Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains	PRJNA1232602	Other	In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.				Iso Seq RNA from Danio rerio	C2 F2 M T		strain:NHGRI2\|isolate:Single paired cross\|breed:Zebrafish\|cultivar:wild type\|ecotype:United States\|age:9 month\|dev stage:adult fish\|collection date:2024 06\|geo loc name:USA\|sex:male\|tissue:testis\|BioSampleModel:Model organism or animal									Iso Seq RNA from testis	C2 F2 M T	C2 F2 M T	The long Read Sequencing libraries was sequenced using PacBio Sequel II			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	PACBIO_SMRT	Sequel II		SRP568323			m84270_240911_150713_s1.skera.flnc.fastq.gz	fastq	103111938047.0	50624762.0	m84270 240911 150713 s1.skera.flnc.fastq.gz	0:2036.79	A:30106378730;C:21760983790;G:23176083069;T:28068492458;N:0	2036		30106378730	21760983790	23176083069	28068492458	0	SRX27895229	SRS24266229	SRA2089085	National Human Genome Research Institute\|Translational and Functional Genomics Branch	National Human Genome Research Institute National Human Genome Research Institute							T	long read	pacbio	pacbio_modern	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2025-03-06	Adult	Adult	Gonad	Reproductive System
34974	34974	SRR32588731	SRX27895220	SRS24266226	SRP568323	PRJNA1232602	Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains	PRJNA1232602	Other	In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.				Iso Seq RNA from Danio rerio	C2 F2 F O32		strain:NHGRI2\|isolate:Single paired cross\|breed:Zebrafish\|cultivar:wild type\|ecotype:United States\|age:9 month\|dev stage:adult fish\|collection date:2024 06\|geo loc name:USA\|sex:female\|tissue:ovary\|BioSampleModel:Model organism or animal									Iso Seq RNA from ovary	C2 F2 F O32	C2 F2 F O32	The long Read Sequencing libraries was sequenced using PacBio Sequel II			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	PACBIO_SMRT	Sequel II		SRP568323			m64467e_240815_161552.hifi_reads.flnc.fastq.gz	fastq	12555748052.0	3350326.0	m64467e 240815 161552.hifi reads.flnc.fastq.gz	0:3747.62	A:3457885256;C:2882310858;G:2971165409;T:3244386529;N:0	3747		3457885256	2882310858	2971165409	3244386529	0	SRX27895220	SRS24266226	SRA2089085	National Human Genome Research Institute\|Translational and Functional Genomics Branch	National Human Genome Research Institute National Human Genome Research Institute							T	long read	pacbio	pacbio_modern	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2025-03-06	Adult	Adult	Gonad	Reproductive System
34975	34975	SRR32588732	SRX27895219	SRS24266221	SRP568323	PRJNA1232602	Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains	PRJNA1232602	Other	In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.				Iso Seq RNA from Danio rerio	C2 F2 F O31		strain:NHGRI2\|isolate:Single paired cross\|breed:Zebrafish\|cultivar:wild type\|ecotype:United States\|age:9 month\|dev stage:adult fish\|collection date:2024 06\|geo loc name:USA\|sex:female\|tissue:Ovary\|BioSampleModel:Model organism or animal									Iso Seq RNA from ovary	C2 F2 F O31	C2 F2 F O31	The long Read Sequencing libraries was sequenced using PacBio Sequel II			RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	PACBIO_SMRT	Sequel II		SRP568323			m84270_240911_210533_s4.skera.flnc.fastq.gz	fastq	91708771607.0	33888263.0	m84270 240911 210533 s4.skera.flnc.fastq.gz	0:2706.21	A:25318206966;C:20635348405;G:21357313254;T:24397902982;N:0	2706		25318206966	20635348405	21357313254	24397902982	0	SRX27895219	SRS24266221	SRA2089085	National Human Genome Research Institute\|Translational and Functional Genomics Branch	National Human Genome Research Institute National Human Genome Research Institute							T	long read	pacbio	pacbio_modern	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2025-03-06	Adult	Adult	Gonad	Reproductive System
36260	36260	SRR062657	SRX025025	SRS085804	SRP003165	PRJNA127881	High throughput sequencing of mRNA from oocyte 1 cell 16/32 cells 128/256 cells 3.5hpf and 5.3hpf zebrafish embryos Wild type; AB line	GSE22830	Transcriptome Analysis	mRNA seq based approach to determine the transcriptome dynamics during early development To study the mechanisms regulating this developmental event in zebrafish we applied RNA deep sequencing technology and generated comprehensive transcriptome profiles of 6 developmental stages from oocyte to early gastrulation. We determined the expression levels of maternal and zygotic transcripts and clustered them based on expression pattern. We identified a large number of novel transcribed regions in un annotated regions of the genome as well as splice variants with an estimated frequency of 40 75% during early zebrafish embryogenesis. Our data constitute a useful resource for developmental studies gene discovery and genome annotation. Overall design: RNA was extracted from pooled embryos of desired stages and one RNA seq library was generated for each sample. Totally 6 stages were selected: Maternal 1cell 16/32 cells 128/256 cells 3.5hpf and 5.3hpf		pubmed:21555364;pubmed:24586560;pubmed:23676078		Maternal	GSM564427		tissue:Unfertilized egg\|background:AB; wild type\|developmental stage:unfertilized eggs	Maternal	ABI pipeline BioScope v1.0.1 Data analysis: The SOLiD generated RNA Seq reads was in 50bp length and an initial filtering process was taken to remove any non desirable contamination sequences such as rRNA tRNA and repeats etc. A seed and extension mapping approach was developed to map the 50bp reads into reference genome zv7 and also into the respective zv7 refGene annotation separately. During mapping of the reads to the refGene annotation a splice junction database fasta file is generated to which the reads are mapped to. This database contains known and putative junction sequences created by taking 46bp from the joining ends of adjacent and non adjacent exons for each gene and putting them together simulating the genomic sequences of known and putative junctions respectively. The first 25bp of the 50bp read was used as the seed for alignment for each read. When an alignment cannot be found using these 25bp seed the seed window is shifted and the next 25bp seed is taken from the 21st to the 45th base of the read. An extension step follows when the seed is able to map and a score generated for each extended base to determine best alignment. A merging step is performed on the genome mapping and splice junction mapping to determine a set of alignments for each read from which a unique alignment is found based on the score generated for these alignments. Mapping parameters: Mapping was done using Applied Biosystems’ SOLiD BioScope alignment for whole transcriptome analysis pipeline. Two mismatches were allowed in the 25bp color space seed sequence with extension alignment performed to find the full mapping location. A score is computed for each mapping location and any location that scored <22 were filtered. Generation of gff and bedgraph files: GFF files were produced by parsing the output BAM format and extracted for unique alignments with score >22. The bedgraph files are then produced with the resulting gff file.	Unfertilized egg	Embryos were frozen at the desired developmental stages and RNAs was extracted for sequencing.	mRNA seq was performed by Mission Biotech Taiwan. SOLiD sequencing libraries were prepared using the Whole Transcriptome Library Preparation for SOLiD™ Sequencing kit ABI according to manufacturer’s instructions. About 200 280 µg of total RNAs were used as starting materials which were subjected to polyA selection using Applied Biosystems PolyA Purist Kit AM1916 fragmentation and library construction using distinct adapters for each library SOLiD Barcoding. From each library equal volumes were pooled together and sequenced in SOLiD3 ABI platform generating 50bp tags.	Zebrafish embryos AB background collected just post fertilization were reared and harvested at desired time points. Unfertilized oocytes were collected by squeezing the abdomen of spawning females. Harvested embryos were snap frozen in liquid nitrogen and stored in −80°C. Total RNA was extracted from whole embryos using Trizol Invitrogen according to manufacturer’s instructions. RNA concentrations were determined using NanoDrop 2000 Thermo Scientific. Integrity of RNA samples were determined using Agilent RNA 6000 Nano chip and size separated using Agilent 2100 Bioanalyzer. Total RNA obtained per 100 embryos at each developmental stage was calculated for data normalization purposes.	background:AB; wild type\|developmental stage:unfertilized eggs	GSM564427	GSM564427: Maternal	GSM564427: Maternal	GSM564427: Maternal	1		GEO Accession:GSM564427	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB SOLiD System 3.0	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP003165					1566199300.0	31323986.0	GSM564427 1	0:50		50							SRX025025	SRS085804	SRA022850	GEO	Computational and Systems Biology, Genome Institute of Singapore	1	0.72688	0.05657	0.876	0.51223	50	B	usable mapping rate	legacy	early	full_length	poly_a	unknown	bulk	unknown	unknown	Singapore	2010-07-08	Zygote	Embryo	Oocyte	Reproductive System
36288	36288	SRR363982	SRX105295	SRS270138	SRP009275	PRJNA148581	Hen1 analysis in zebrafish	GSE33582	Transcriptome Analysis	small RNA libraries from wild type and Hen1 mutant testes were made with either polyA tailing VASAGFPHen1minus/plus or adapter ligation Hen1Testis and WTTestis and sequenced on an Illumina GAII platform. Overall design: RNA was isolated from total testis tissue of both Hen1 wildtype and Hen1 mutant animals. post size selection from gel the small RNA libraries wre made.		pubmed:20859253		hen1 mutant polyA	GSM830244		source name:testis\|strain:TL\|genotype/variation:Hen1 mutant\|tissue:testis\|small rna library prep method:polyA tailing	hen1 mutant polyA	three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the zebrafish genome Zv8	testis		Small RNAs in the size range of 19 31 bases were excised from a denaturing gel. RNA was polyA tailed using polyA polymerase followed by ligation of a RNA adaptor to the five prime phosphate of the small RNAs. First strand cDNA synthesis was performed using an oligodT linker primer and M MLV RNase H reverse transcriptase. post amplification the cDNA was sent for sequencing on an Illumina/Solexa platform.		strain:TL\|genotype/variation:Hen1 mutant\|tissue:testis\|small rna library prep method:polyA tailing	GSM830244	GSM830244: hen1 mutant polyA	GSM830244: hen1 mutant polyA	GSM830244: hen1 mutant polyA	1		GEO Accession:GSM830244	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer II	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>44</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP009275		read name barcode proc directive:ignore	VASAGFPHEN1minusMALE.fastq	fastq	267208964.0	6072931.0	GSM830244 1	0:44	A:143478691;C:30051676;G:33682677;T:59883224;N:112696	44		143478691	30051676	33682677	59883224	112696	SRX105295	SRS270138	SRA047996	GEO	European Research Institute for the Biology of Ageing, University Medical Center Groningen	1	0.01616	0.01033	0.99381	0.76337	44	B	usable mapping rate	illumina	early_illumina	unknown	poly_a	unknown	bulk	unknown	unknown	Netherlands	2011-11-09	Undetermined	Undetermined	Gonad	Reproductive System
36361	36361	SRR489488	SRX143565	SRS310286	SRP012376	PRJNA160143	Extensive alternative polyadenylation during zebrafish development	GSE37453	Transcriptome Analysis	The post transcriptional fate of messenger RNAs mRNAs is largely dictated by their three prime' untranslated regions three prime'UTRs which are defined by cleavage and polyadenylation CPA of pre mRNAs. We used polyA position profiling by sequencing 3P Seq to map polyA sites at eight developmental stages and tissues in the zebrafish. Analysis of over 60 million 3P Seq reads substantially increased and improved existing three prime'UTR annotations resulting in confidently identified three prime'UTRs for more than 78.79% of the annotated protein coding genes in zebrafish. Most zebrafish genes undergo alternative CPA with more than a thousand genes using different dominant three prime'UTRs at different stages. three prime'UTRs tend to be shortest in the ovaries and longest in the brain. Isoforms with some of the shortest three prime'UTRs are highly expressed in the ovary yet absent in the maternally contributed RNAs of the embryo perhaps because their three prime'UTRs are too short to accommodate a uridine rich motif required for stability of the maternal mRNA. At two hpf thousands of unique polyA sites appear at locations lacking a typical polyadenylation signal which suggests a wave of widespread cytoplasmic polyadenylation of mRNA degradation intermediates. Our insights into the identities formation and evolution of zebrafish three prime'UTRs provide a resource for studying gene regulation during vertebrate development. Overall design: 3P Seq was used to map the three prime' ends of protein coding genes in the zebrafish genome		pubmed:22722342		3P Seq Testis	GSM919971		source name:male adults\|genotype/variation:wild type\|tissue:testis\|development stage:adult	3P Seq Testis	For 3P Seq: Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. The BED file is as in Jan et al. GSE24924 For 3P PE Seq: In each read pair read #1 captured the three prime end of the polyA tail in the antisense orientation and read #2 captured a portion of the three prime region of the transcript and occasionally the beginning of the polyA tail in the sense orientation. Read #2 began with an adapter of 26 bases. Reads with more than 10 mismatches to the adapter were discarded and the first 26 bases were removed before further processing. A read pair was considered informative only if read #1 began with Ts and read #2 contained 2–39 terminal As. post leading Ts and terminal As were removed from reads #1 and #2 respectively they were mapped to the genome using Bowtie allowing for up to two mismatches and requiring a unique mapping position in the zebrafish genome. The length of the tail encoded in read #2 was defined as the maximum number of trailing As allowing for up to one mismatch. Only cases in which this number was larger than the number of As encoded in the genome at the predicted cleavage position by at least 2 bases were carried forward. Cleavage and polyadenylation position was defined as the last non A base in read #2. The length of the polyA tail at that position was estimated using the corresponding read #1 and defined as the maximal i for which >90% of the bases in the first i bases of read #1 were Ts. This criterion was used to allow for some sequencing errors expected when sequencing long homopolymers. Genome build: danRer7 Supplementary files format and content: The .bed files contain the positions where 3P Seq reads were mapped and the name of each track is the …	male adults	Ovaries and testes were obtained as described in Gupta and Mullins 2010.	3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html	Zebrafish embryos or adults grown under standard condition	genotype/variation:wild type\|tissue:testis\|developmental stage:adult	GSM919971	GSM919971: 3P Seq Testis; Danio rerio; RNA Seq	GSM919971 1	GSM919971: 3P Seq Testis	1		GEO Accession:GSM919971	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer II	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP012376			3P_Seq_Testis.fastq	fastq	633839040.0	17606640.0	GSM919971 r1	0:36	A:250493743;C:111846021;G:97558731;T:173764035;N:176510	36		250493743	111846021	97558731	173764035	176510	SRX143565	SRS310286	SRA051955	GEO	Whitehead Institute for Biomedical Research	1	0.56499	0.1059	0.72468	0.46158	36	B	usable mapping rate	illumina	early_illumina	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2012-04-20	Adult	Adult	Gonad	Reproductive System
36362	36362	SRR489487	SRX143564	SRS310285	SRP012376	PRJNA160143	Extensive alternative polyadenylation during zebrafish development	GSE37453	Transcriptome Analysis	The post transcriptional fate of messenger RNAs mRNAs is largely dictated by their three prime' untranslated regions three prime'UTRs which are defined by cleavage and polyadenylation CPA of pre mRNAs. We used polyA position profiling by sequencing 3P Seq to map polyA sites at eight developmental stages and tissues in the zebrafish. Analysis of over 60 million 3P Seq reads substantially increased and improved existing three prime'UTR annotations resulting in confidently identified three prime'UTRs for more than 78.79% of the annotated protein coding genes in zebrafish. Most zebrafish genes undergo alternative CPA with more than a thousand genes using different dominant three prime'UTRs at different stages. three prime'UTRs tend to be shortest in the ovaries and longest in the brain. Isoforms with some of the shortest three prime'UTRs are highly expressed in the ovary yet absent in the maternally contributed RNAs of the embryo perhaps because their three prime'UTRs are too short to accommodate a uridine rich motif required for stability of the maternal mRNA. At two hpf thousands of unique polyA sites appear at locations lacking a typical polyadenylation signal which suggests a wave of widespread cytoplasmic polyadenylation of mRNA degradation intermediates. Our insights into the identities formation and evolution of zebrafish three prime'UTRs provide a resource for studying gene regulation during vertebrate development. Overall design: 3P Seq was used to map the three prime' ends of protein coding genes in the zebrafish genome		pubmed:22722342		3P Seq Ovary	GSM919970		source name:female adults\|genotype/variation:wild type\|tissue:ovary\|development stage:adult	3P Seq Ovary	For 3P Seq: Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. The BED file is as in Jan et al. GSE24924 For 3P PE Seq: In each read pair read #1 captured the three prime end of the polyA tail in the antisense orientation and read #2 captured a portion of the three prime region of the transcript and occasionally the beginning of the polyA tail in the sense orientation. Read #2 began with an adapter of 26 bases. Reads with more than 10 mismatches to the adapter were discarded and the first 26 bases were removed before further processing. A read pair was considered informative only if read #1 began with Ts and read #2 contained 2–39 terminal As. post leading Ts and terminal As were removed from reads #1 and #2 respectively they were mapped to the genome using Bowtie allowing for up to two mismatches and requiring a unique mapping position in the zebrafish genome. The length of the tail encoded in read #2 was defined as the maximum number of trailing As allowing for up to one mismatch. Only cases in which this number was larger than the number of As encoded in the genome at the predicted cleavage position by at least 2 bases were carried forward. Cleavage and polyadenylation position was defined as the last non A base in read #2. The length of the polyA tail at that position was estimated using the corresponding read #1 and defined as the maximal i for which >90% of the bases in the first i bases of read #1 were Ts. This criterion was used to allow for some sequencing errors expected when sequencing long homopolymers. Genome build: danRer7 Supplementary files format and content: The .bed files contain the positions where 3P Seq reads were mapped and the name of each track is the …	female adults	Ovaries and testes were obtained as described in Gupta and Mullins 2010.	3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html	Zebrafish embryos or adults grown under standard condition	genotype/variation:wild type\|tissue:ovary\|developmental stage:adult	GSM919970	GSM919970: 3P Seq Ovary; Danio rerio; RNA Seq	GSM919970 1	GSM919970: 3P Seq Ovary	1		GEO Accession:GSM919970	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer II	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP012376			3P_Seq_Ovary.fastq	fastq	644470380.0	17901955.0	GSM919970 r1	0:36	A:263871252;C:97757369;G:94972134;T:187683515;N:186110	36		263871252	97757369	94972134	187683515	186110	SRX143564	SRS310285	SRA051955	GEO	Whitehead Institute for Biomedical Research	1	0.51356	0.04868	0.821	0.48788	36	B	usable mapping rate	illumina	early_illumina	3prime	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2012-04-20	Adult	Adult	Gonad	Reproductive System
40962	40962	SRR3470786	SRX1738401	SRS1418771	SRP074244	PRJNA320266	Dietary intake influences fertility and offspring development in zebrafish.	GSE81007	Transcriptome Analysis	We report that increased nutrient availability increases breeding success and egg production. RNA seq analysis revealed that parental diet altered the expression of metabolic genes in the unfertilized eggs. Offspring from the differentially fed parents showed altered survival and energy expenditure as adults. Overall design: RNA from unfertilized eggs post two parental diets.		pubmed:27870856		60mg arm 3	GSM2140605		source name:Unfertilized eggs\|strain:In house AB/Pet shop\|tissue:Unfertilized eggs\|FISH age:9 mpf\|treatment arm:60 mg	60mg arm 3	Sequence reads were filtered for quality using trimgalore. Reads were then mapped to the zebrafish genome using tophat v2.0.9 then assembled and merged with cufflinks v2.2.0 and cuffmerge respectively. Differentially expressed transcripts were determined using cuffdiff v2.2.0. Gene ontology was assessed using BinGO 3.0.3 a plugin for cytoscape v3.3.0. Genome build: Zv9	Unfertilized eggs	Zebrafish were fed either 5 mg or 60 mg Artemia each day for eight weeks.	The eggs were transferred to tube containing RA1 buffer Macherey Nagel cat. 740955.250 with b mercaptoethanol and stored at 80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel cat. 740955.250 and bound and eluted with columns 17 23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish were maintained under standard conditions	strain:In house AB/Pet shop\|tissue:Unfertilized eggs\|FISH age:9 mpf\|treatment arm:60 mg	GSM2140605	GSM2140605: 60mg arm 3; Danio rerio; RNA Seq	GSM2140605		1	The eggs were transferred to tube containing RA1 buffer Macherey Nagel cat. 740955.250 with b mercaptoethanol and stored at 80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel cat. 740955.250 and bound and eluted with columns 17 23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2140605	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP074244			60mg-arm-3.fastq.gz	fastq	2353067800.0	23530678.0	GSM2140605 r1	0:100	A:550921675;C:559384489;G:553530174;T:689218350;N:13112	100		550921675	559384489	553530174	689218350	13112	SRX1738401	SRS1418771	SRA422860	GEO	Chromosome Structure and Development Group, Department of Pathology, University of Otago	1	0.95538	0.04454	0.7512	0.62731	100	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2016-05-02	Multi-stage	Multi-stage	Oocyte	Reproductive System
40963	40963	SRR3470785	SRX1738399	SRS1418770	SRP074244	PRJNA320266	Dietary intake influences fertility and offspring development in zebrafish.	GSE81007	Transcriptome Analysis	We report that increased nutrient availability increases breeding success and egg production. RNA seq analysis revealed that parental diet altered the expression of metabolic genes in the unfertilized eggs. Offspring from the differentially fed parents showed altered survival and energy expenditure as adults. Overall design: RNA from unfertilized eggs post two parental diets.		pubmed:27870856		60mg arm 2	GSM2140604		source name:Unfertilized eggs\|strain:In house AB/Pet shop\|tissue:Unfertilized eggs\|FISH age:9 mpf\|treatment arm:60 mg	60mg arm 2	Sequence reads were filtered for quality using trimgalore. Reads were then mapped to the zebrafish genome using tophat v2.0.9 then assembled and merged with cufflinks v2.2.0 and cuffmerge respectively. Differentially expressed transcripts were determined using cuffdiff v2.2.0. Gene ontology was assessed using BinGO 3.0.3 a plugin for cytoscape v3.3.0. Genome build: Zv9	Unfertilized eggs	Zebrafish were fed either 5 mg or 60 mg Artemia each day for eight weeks.	The eggs were transferred to tube containing RA1 buffer Macherey Nagel cat. 740955.250 with b mercaptoethanol and stored at 80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel cat. 740955.250 and bound and eluted with columns 17 23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish were maintained under standard conditions	strain:In house AB/Pet shop\|tissue:Unfertilized eggs\|FISH age:9 mpf\|treatment arm:60 mg	GSM2140604	GSM2140604: 60mg arm 2; Danio rerio; RNA Seq	GSM2140604		1	The eggs were transferred to tube containing RA1 buffer Macherey Nagel cat. 740955.250 with b mercaptoethanol and stored at 80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel cat. 740955.250 and bound and eluted with columns 17 23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2140604	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP074244			60mg-arm-2.fastq.gz	fastq	2552419200.0	25524192.0	GSM2140604 r1	0:100	A:598028827;C:604381782;G:600136410;T:749858137;N:14044	100		598028827	604381782	600136410	749858137	14044	SRX1738399	SRS1418770	SRA422860	GEO	Chromosome Structure and Development Group, Department of Pathology, University of Otago	1	0.95953	0.04033	0.75408	0.63549	100	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2016-05-02	Multi-stage	Multi-stage	Oocyte	Reproductive System
40964	40964	SRR3470784	SRX1738397	SRS1418769	SRP074244	PRJNA320266	Dietary intake influences fertility and offspring development in zebrafish.	GSE81007	Transcriptome Analysis	We report that increased nutrient availability increases breeding success and egg production. RNA seq analysis revealed that parental diet altered the expression of metabolic genes in the unfertilized eggs. Offspring from the differentially fed parents showed altered survival and energy expenditure as adults. Overall design: RNA from unfertilized eggs post two parental diets.		pubmed:27870856		60mg arm 1	GSM2140603		source name:Unfertilized eggs\|strain:In house AB/Pet shop\|tissue:Unfertilized eggs\|FISH age:9 mpf\|treatment arm:60 mg	60mg arm 1	Sequence reads were filtered for quality using trimgalore. Reads were then mapped to the zebrafish genome using tophat v2.0.9 then assembled and merged with cufflinks v2.2.0 and cuffmerge respectively. Differentially expressed transcripts were determined using cuffdiff v2.2.0. Gene ontology was assessed using BinGO 3.0.3 a plugin for cytoscape v3.3.0. Genome build: Zv9	Unfertilized eggs	Zebrafish were fed either 5 mg or 60 mg Artemia each day for eight weeks.	The eggs were transferred to tube containing RA1 buffer Macherey Nagel cat. 740955.250 with b mercaptoethanol and stored at 80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel cat. 740955.250 and bound and eluted with columns 17 23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish were maintained under standard conditions	strain:In house AB/Pet shop\|tissue:Unfertilized eggs\|FISH age:9 mpf\|treatment arm:60 mg	GSM2140603	GSM2140603: 60mg arm 1; Danio rerio; RNA Seq	GSM2140603		1	The eggs were transferred to tube containing RA1 buffer Macherey Nagel cat. 740955.250 with b mercaptoethanol and stored at 80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel cat. 740955.250 and bound and eluted with columns 17 23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2140603	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP074244			60mg-arm-1.fastq.gz	fastq	2471843300.0	24718433.0	GSM2140603 r1	0:100	A:578536744;C:593318438;G:586674975;T:713299111;N:14032	100		578536744	593318438	586674975	713299111	14032	SRX1738397	SRS1418769	SRA422860	GEO	Chromosome Structure and Development Group, Department of Pathology, University of Otago	1	0.95474	0.04276	0.75625	0.61194	100	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2016-05-02	Multi-stage	Multi-stage	Oocyte	Reproductive System
40965	40965	SRR3470783	SRX1738395	SRS1418767	SRP074244	PRJNA320266	Dietary intake influences fertility and offspring development in zebrafish.	GSE81007	Transcriptome Analysis	We report that increased nutrient availability increases breeding success and egg production. RNA seq analysis revealed that parental diet altered the expression of metabolic genes in the unfertilized eggs. Offspring from the differentially fed parents showed altered survival and energy expenditure as adults. Overall design: RNA from unfertilized eggs post two parental diets.		pubmed:27870856		5mg arm 3	GSM2140602		source name:Unfertilized eggs\|strain:In house AB/Pet shop\|tissue:Unfertilized eggs\|FISH age:9 mpf\|treatment arm:5 mg	5mg arm 3	Sequence reads were filtered for quality using trimgalore. Reads were then mapped to the zebrafish genome using tophat v2.0.9 then assembled and merged with cufflinks v2.2.0 and cuffmerge respectively. Differentially expressed transcripts were determined using cuffdiff v2.2.0. Gene ontology was assessed using BinGO 3.0.3 a plugin for cytoscape v3.3.0. Genome build: Zv9	Unfertilized eggs	Zebrafish were fed either 5 mg or 60 mg Artemia each day for eight weeks.	The eggs were transferred to tube containing RA1 buffer Macherey Nagel cat. 740955.250 with b mercaptoethanol and stored at 80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel cat. 740955.250 and bound and eluted with columns 17 23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish were maintained under standard conditions	strain:In house AB/Pet shop\|tissue:Unfertilized eggs\|FISH age:9 mpf\|treatment arm:5 mg	GSM2140602	GSM2140602: 5mg arm 3; Danio rerio; RNA Seq	GSM2140602		1	The eggs were transferred to tube containing RA1 buffer Macherey Nagel cat. 740955.250 with b mercaptoethanol and stored at 80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel cat. 740955.250 and bound and eluted with columns 17 23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2140602	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP074244			5mg-arm-3.fastq.gz	fastq	2562336500.0	25623365.0	GSM2140602 r1	0:100	A:599122965;C:614407524;G:605967391;T:742824547;N:14073	100		599122965	614407524	605967391	742824547	14073	SRX1738395	SRS1418767	SRA422860	GEO	Chromosome Structure and Development Group, Department of Pathology, University of Otago	1	0.95071	0.0461	0.74483	0.61788	100	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2016-05-02	Multi-stage	Multi-stage	Oocyte	Reproductive System
40966	40966	SRR3470782	SRX1738393	SRS1418765	SRP074244	PRJNA320266	Dietary intake influences fertility and offspring development in zebrafish.	GSE81007	Transcriptome Analysis	We report that increased nutrient availability increases breeding success and egg production. RNA seq analysis revealed that parental diet altered the expression of metabolic genes in the unfertilized eggs. Offspring from the differentially fed parents showed altered survival and energy expenditure as adults. Overall design: RNA from unfertilized eggs post two parental diets.		pubmed:27870856		5mg arm 2	GSM2140601		source name:Unfertilized eggs\|strain:In house AB/Pet shop\|tissue:Unfertilized eggs\|FISH age:9 mpf\|treatment arm:5 mg	5mg arm 2	Sequence reads were filtered for quality using trimgalore. Reads were then mapped to the zebrafish genome using tophat v2.0.9 then assembled and merged with cufflinks v2.2.0 and cuffmerge respectively. Differentially expressed transcripts were determined using cuffdiff v2.2.0. Gene ontology was assessed using BinGO 3.0.3 a plugin for cytoscape v3.3.0. Genome build: Zv9	Unfertilized eggs	Zebrafish were fed either 5 mg or 60 mg Artemia each day for eight weeks.	The eggs were transferred to tube containing RA1 buffer Macherey Nagel cat. 740955.250 with b mercaptoethanol and stored at 80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel cat. 740955.250 and bound and eluted with columns 17 23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish were maintained under standard conditions	strain:In house AB/Pet shop\|tissue:Unfertilized eggs\|FISH age:9 mpf\|treatment arm:5 mg	GSM2140601	GSM2140601: 5mg arm 2; Danio rerio; RNA Seq	GSM2140601		1	The eggs were transferred to tube containing RA1 buffer Macherey Nagel cat. 740955.250 with b mercaptoethanol and stored at 80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel cat. 740955.250 and bound and eluted with columns 17 23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2140601	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP074244			5mg-arm-2.fastq.gz	fastq	2841710700.0	28417107.0	GSM2140601 r1	0:100	A:663485391;C:679416584;G:665850494;T:832942768;N:15463	100		663485391	679416584	665850494	832942768	15463	SRX1738393	SRS1418765	SRA422860	GEO	Chromosome Structure and Development Group, Department of Pathology, University of Otago	1	0.94998	0.04837	0.75442	0.63571	100	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2016-05-02	Multi-stage	Multi-stage	Oocyte	Reproductive System
40967	40967	SRR3470781	SRX1738391	SRS1418764	SRP074244	PRJNA320266	Dietary intake influences fertility and offspring development in zebrafish.	GSE81007	Transcriptome Analysis	We report that increased nutrient availability increases breeding success and egg production. RNA seq analysis revealed that parental diet altered the expression of metabolic genes in the unfertilized eggs. Offspring from the differentially fed parents showed altered survival and energy expenditure as adults. Overall design: RNA from unfertilized eggs post two parental diets.		pubmed:27870856		5mg arm 1	GSM2140600		source name:Unfertilized eggs\|strain:In house AB/Pet shop\|tissue:Unfertilized eggs\|FISH age:9 mpf\|treatment arm:5 mg	5mg arm 1	Sequence reads were filtered for quality using trimgalore. Reads were then mapped to the zebrafish genome using tophat v2.0.9 then assembled and merged with cufflinks v2.2.0 and cuffmerge respectively. Differentially expressed transcripts were determined using cuffdiff v2.2.0. Gene ontology was assessed using BinGO 3.0.3 a plugin for cytoscape v3.3.0. Genome build: Zv9	Unfertilized eggs	Zebrafish were fed either 5 mg or 60 mg Artemia each day for eight weeks.	The eggs were transferred to tube containing RA1 buffer Macherey Nagel cat. 740955.250 with b mercaptoethanol and stored at 80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel cat. 740955.250 and bound and eluted with columns 17 23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish were maintained under standard conditions	strain:In house AB/Pet shop\|tissue:Unfertilized eggs\|FISH age:9 mpf\|treatment arm:5 mg	GSM2140600	GSM2140600: 5mg arm 1; Danio rerio; RNA Seq	GSM2140600		1	The eggs were transferred to tube containing RA1 buffer Macherey Nagel cat. 740955.250 with b mercaptoethanol and stored at 80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel cat. 740955.250 and bound and eluted with columns 17 23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2140600	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP074244			5mg-arm-1.fastq.gz	fastq	2409548800.0	24095488.0	GSM2140600 r1	0:100	A:519836883;C:638777587;G:641445656;T:609475335;N:13339	100		519836883	638777587	641445656	609475335	13339	SRX1738391	SRS1418764	SRA422860	GEO	Chromosome Structure and Development Group, Department of Pathology, University of Otago	1	0.88003	0.04264	0.76138	0.66721	100	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2016-05-02	Multi-stage	Multi-stage	Oocyte	Reproductive System
41175	41175	SRR3923687	SRX1950218	SRS1564979	SRP078537	PRJNA329141	Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis	GSE84436	Transcriptome Analysis	Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.		pubmed:27566230		Trilostane+Fsh 6	GSM2236119		source name:Testis\|tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	Trilostane+Fsh 6	Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	GSM2236119	GSM2236119: Trilostane+Fsh 6; Danio rerio; RNA Seq	GSM2236119		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2236119	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP078537			Seq19_H9PG8ADXX_CTGAAGCT-GTACTGAC_L001_R1_001.fastq.gz	fastq	541196550.0	10823931.0	GSM2236119 r1	0:50	A:129904818;C:128871362;G:125784183;T:151841105;N:4795082	50		129904818	128871362	125784183	151841105	4795082	SRX1950218	SRS1564979	SRA440585	GEO	Reproductive Biology, Biology, Utrecht University	1	0.83528	0.26943	0.65632	0.56402	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-07-14	Adult	Adult	Gonad	Reproductive System
41176	41176	SRR3923688	SRX1950218	SRS1564979	SRP078537	PRJNA329141	Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis	GSE84436	Transcriptome Analysis	Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.		pubmed:27566230		Trilostane+Fsh 6	GSM2236119		source name:Testis\|tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	Trilostane+Fsh 6	Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	GSM2236119	GSM2236119: Trilostane+Fsh 6; Danio rerio; RNA Seq	GSM2236119		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2236119	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP078537			Seq19_H9PG8ADXX_CTGAAGCT-GTACTGAC_L002_R1_001.fastq.gz	fastq	540752550.0	10815051.0	GSM2236119 r2	0:50	A:129870926;C:128702724;G:125668527;T:151723226;N:4787147	50		129870926	128702724	125668527	151723226	4787147	SRX1950218	SRS1564979	SRA440585	GEO	Reproductive Biology, Biology, Utrecht University	1	0.83561	0.26923	0.65658	0.5633	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-07-14	Adult	Adult	Gonad	Reproductive System
41177	41177	SRR3923685	SRX1950217	SRS1564978	SRP078537	PRJNA329141	Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis	GSE84436	Transcriptome Analysis	Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.		pubmed:27566230		Trilostane+Fsh 5	GSM2236118		source name:Testis\|tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	Trilostane+Fsh 5	Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	GSM2236118	GSM2236118: Trilostane+Fsh 5; Danio rerio; RNA Seq	GSM2236118		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2236118	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP078537			Seq18_H9PG8ADXX_ATTCAGAA-GTACTGAC_L001_R1_001.fastq.gz	fastq	536259700.0	10725194.0	GSM2236118 r1	0:50	A:132683158;C:124371530;G:118570874;T:155804755;N:4829383	50		132683158	124371530	118570874	155804755	4829383	SRX1950217	SRS1564978	SRA440585	GEO	Reproductive Biology, Biology, Utrecht University	1	0.86166	0.28405	0.66085	0.56844	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-07-14	Adult	Adult	Gonad	Reproductive System
41178	41178	SRR3923686	SRX1950217	SRS1564978	SRP078537	PRJNA329141	Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis	GSE84436	Transcriptome Analysis	Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.		pubmed:27566230		Trilostane+Fsh 5	GSM2236118		source name:Testis\|tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	Trilostane+Fsh 5	Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	GSM2236118	GSM2236118: Trilostane+Fsh 5; Danio rerio; RNA Seq	GSM2236118		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2236118	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP078537			Seq18_H9PG8ADXX_ATTCAGAA-GTACTGAC_L002_R1_001.fastq.gz	fastq	536614850.0	10732297.0	GSM2236118 r2	0:50	A:132824083;C:124387998;G:118657068;T:155922787;N:4822914	50		132824083	124387998	118657068	155922787	4822914	SRX1950217	SRS1564978	SRA440585	GEO	Reproductive Biology, Biology, Utrecht University	1	0.86253	0.2872	0.66176	0.56675	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-07-14	Adult	Adult	Gonad	Reproductive System
41179	41179	SRR3923683	SRX1950216	SRS1564977	SRP078537	PRJNA329141	Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis	GSE84436	Transcriptome Analysis	Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.		pubmed:27566230		Trilostane+Fsh 4	GSM2236117		source name:Testis\|tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	Trilostane+Fsh 4	Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	GSM2236117	GSM2236117: Trilostane+Fsh 4; Danio rerio; RNA Seq	GSM2236117		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2236117	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP078537			Seq16_H9PG8ADXX_CGCTCATT-GTACTGAC_L001_R1_001.fastq.gz	fastq	427009700.0	8540194.0	GSM2236117 r1	0:50	A:104823398;C:99767068;G:94526860;T:124062805;N:3829569	50		104823398	99767068	94526860	124062805	3829569	SRX1950216	SRS1564977	SRA440585	GEO	Reproductive Biology, Biology, Utrecht University	1	0.86391	0.29478	0.65476	0.47031	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-07-14	Adult	Adult	Gonad	Reproductive System
41180	41180	SRR3923684	SRX1950216	SRS1564977	SRP078537	PRJNA329141	Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis	GSE84436	Transcriptome Analysis	Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.		pubmed:27566230		Trilostane+Fsh 4	GSM2236117		source name:Testis\|tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	Trilostane+Fsh 4	Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	GSM2236117	GSM2236117: Trilostane+Fsh 4; Danio rerio; RNA Seq	GSM2236117		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2236117	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP078537			Seq16_H9PG8ADXX_CGCTCATT-GTACTGAC_L002_R1_001.fastq.gz	fastq	425476900.0	8509538.0	GSM2236117 r2	0:50	A:104473554;C:99368446;G:94196508;T:123623942;N:3814450	50		104473554	99368446	94196508	123623942	3814450	SRX1950216	SRS1564977	SRA440585	GEO	Reproductive Biology, Biology, Utrecht University	1	0.86395	0.29677	0.65736	0.46962	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-07-14	Adult	Adult	Gonad	Reproductive System
41181	41181	SRR3923681	SRX1950215	SRS1564976	SRP078537	PRJNA329141	Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis	GSE84436	Transcriptome Analysis	Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.		pubmed:27566230		Trilostane+Fsh 3	GSM2236116		source name:Testis\|tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	Trilostane+Fsh 3	Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	GSM2236116	GSM2236116: Trilostane+Fsh 3; Danio rerio; RNA Seq	GSM2236116		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2236116	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP078537			Seq8_H9PG8ADXX_TCCGCGAA-CAGGACGT_L001_R1_001.fastq.gz	fastq	547479650.0	10949593.0	GSM2236116 r1	0:50	A:132619117;C:134226431;G:118412018;T:157542627;N:4679457	50		132619117	134226431	118412018	157542627	4679457	SRX1950215	SRS1564976	SRA440585	GEO	Reproductive Biology, Biology, Utrecht University	1	0.9055	0.32136	0.66793	0.60282	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-07-14	Adult	Adult	Gonad	Reproductive System
41182	41182	SRR3923682	SRX1950215	SRS1564976	SRP078537	PRJNA329141	Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis	GSE84436	Transcriptome Analysis	Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.		pubmed:27566230		Trilostane+Fsh 3	GSM2236116		source name:Testis\|tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	Trilostane+Fsh 3	Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	GSM2236116	GSM2236116: Trilostane+Fsh 3; Danio rerio; RNA Seq	GSM2236116		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2236116	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP078537			Seq8_H9PG8ADXX_TCCGCGAA-CAGGACGT_L002_R1_001.fastq.gz	fastq	548145550.0	10962911.0	GSM2236116 r2	0:50	A:132852947;C:134322795;G:118563196;T:157723665;N:4682947	50		132852947	134322795	118563196	157723665	4682947	SRX1950215	SRS1564976	SRA440585	GEO	Reproductive Biology, Biology, Utrecht University	1	0.90629	0.3224	0.67079	0.59076	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-07-14	Adult	Adult	Gonad	Reproductive System
41183	41183	SRR3923679	SRX1950214	SRS1564975	SRP078537	PRJNA329141	Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis	GSE84436	Transcriptome Analysis	Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.		pubmed:27566230		Trilostane+Fsh 2	GSM2236115		source name:Testis\|tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	Trilostane+Fsh 2	Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	GSM2236115	GSM2236115: Trilostane+Fsh 2; Danio rerio; RNA Seq	GSM2236115		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2236115	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP078537			Seq6_H9PG8ADXX_TAATGCGC-CAGGACGT_L001_R1_001.fastq.gz	fastq	483539450.0	9670789.0	GSM2236115 r1	0:50	A:113342249;C:121843102;G:107743374;T:136575001;N:4035724	50		113342249	121843102	107743374	136575001	4035724	SRX1950214	SRS1564975	SRA440585	GEO	Reproductive Biology, Biology, Utrecht University	1	0.91137	0.3309	0.67945	0.55402	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-07-14	Adult	Adult	Gonad	Reproductive System
41184	41184	SRR3923680	SRX1950214	SRS1564975	SRP078537	PRJNA329141	Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis	GSE84436	Transcriptome Analysis	Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.		pubmed:27566230		Trilostane+Fsh 2	GSM2236115		source name:Testis\|tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	Trilostane+Fsh 2	Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	GSM2236115	GSM2236115: Trilostane+Fsh 2; Danio rerio; RNA Seq	GSM2236115		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2236115	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP078537			Seq6_H9PG8ADXX_TAATGCGC-CAGGACGT_L002_R1_001.fastq.gz	fastq	483032050.0	9660641.0	GSM2236115 r2	0:50	A:113263999;C:121692767;G:107625313;T:136421502;N:4028469	50		113263999	121692767	107625313	136421502	4028469	SRX1950214	SRS1564975	SRA440585	GEO	Reproductive Biology, Biology, Utrecht University	1	0.9125	0.32793	0.68138	0.54622	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-07-14	Adult	Adult	Gonad	Reproductive System
41185	41185	SRR3923677	SRX1950213	SRS1564974	SRP078537	PRJNA329141	Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis	GSE84436	Transcriptome Analysis	Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.		pubmed:27566230		Trilostane+Fsh 1	GSM2236114		source name:Testis\|tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	Trilostane+Fsh 1	Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	GSM2236114	GSM2236114: Trilostane+Fsh 1; Danio rerio; RNA Seq	GSM2236114		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2236114	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP078537			Seq4_H9PG8ADXX_GAGATTCC-CAGGACGT_L001_R1_001.fastq.gz	fastq	657366700.0	13147334.0	GSM2236114 r1	0:50	A:167604847;C:149043342;G:139125980;T:195616217;N:5976314	50		167604847	149043342	139125980	195616217	5976314	SRX1950213	SRS1564974	SRA440585	GEO	Reproductive Biology, Biology, Utrecht University	1	0.85723	0.34006	0.65415	0.46117	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-07-14	Adult	Adult	Gonad	Reproductive System
41186	41186	SRR3923678	SRX1950213	SRS1564974	SRP078537	PRJNA329141	Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis	GSE84436	Transcriptome Analysis	Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.		pubmed:27566230		Trilostane+Fsh 1	GSM2236114		source name:Testis\|tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	Trilostane+Fsh 1	Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	GSM2236114	GSM2236114: Trilostane+Fsh 1; Danio rerio; RNA Seq	GSM2236114		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2236114	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP078537			Seq4_H9PG8ADXX_GAGATTCC-CAGGACGT_L002_R1_001.fastq.gz	fastq	657335800.0	13146716.0	GSM2236114 r2	0:50	A:167683325;C:148965849;G:139104499;T:195605431;N:5976696	50		167683325	148965849	139104499	195605431	5976696	SRX1950213	SRS1564974	SRA440585	GEO	Reproductive Biology, Biology, Utrecht University	1	0.85828	0.33726	0.65212	0.46064	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-07-14	Adult	Adult	Gonad	Reproductive System
41187	41187	SRR3923675	SRX1950212	SRS1564973	SRP078537	PRJNA329141	Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis	GSE84436	Transcriptome Analysis	Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.		pubmed:27566230		Trilostane 6	GSM2236113		source name:Testis\|tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	Trilostane 6	Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	GSM2236113	GSM2236113: Trilostane 6; Danio rerio; RNA Seq	GSM2236113		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2236113	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP078537			Seq23_H9PG8ADXX_TCTCGCGC-GTACTGAC_L001_R1_001.fastq.gz	fastq	473414850.0	9468297.0	GSM2236113 r1	0:50	A:115132784;C:111560620;G:107691623;T:134806360;N:4223463	50		115132784	111560620	107691623	134806360	4223463	SRX1950212	SRS1564973	SRA440585	GEO	Reproductive Biology, Biology, Utrecht University	1	0.82776	0.27832	0.65922	0.56166	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-07-14	Adult	Adult	Gonad	Reproductive System
41188	41188	SRR3923676	SRX1950212	SRS1564973	SRP078537	PRJNA329141	Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis	GSE84436	Transcriptome Analysis	Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.		pubmed:27566230		Trilostane 6	GSM2236113		source name:Testis\|tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	Trilostane 6	Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	GSM2236113	GSM2236113: Trilostane 6; Danio rerio; RNA Seq	GSM2236113		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2236113	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP078537			Seq23_H9PG8ADXX_TCTCGCGC-GTACTGAC_L002_R1_001.fastq.gz	fastq	471843300.0	9436866.0	GSM2236113 r2	0:50	A:114789047;C:111198690;G:107327397;T:134316769;N:4211397	50		114789047	111198690	107327397	134316769	4211397	SRX1950212	SRS1564973	SRA440585	GEO	Reproductive Biology, Biology, Utrecht University	1	0.82475	0.28061	0.65914	0.56084	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-07-14	Adult	Adult	Gonad	Reproductive System
41189	41189	SRR3923673	SRX1950211	SRS1564972	SRP078537	PRJNA329141	Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis	GSE84436	Transcriptome Analysis	Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.		pubmed:27566230		Trilostane 5	GSM2236112		source name:Testis\|tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	Trilostane 5	Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	GSM2236112	GSM2236112: Trilostane 5; Danio rerio; RNA Seq	GSM2236112		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2236112	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP078537			Seq22_H9PG8ADXX_CGGCTATG-GTACTGAC_L001_R1_001.fastq.gz	fastq	454002550.0	9080051.0	GSM2236112 r1	0:50	A:110121161;C:107184608;G:104060594;T:128567586;N:4068601	50		110121161	107184608	104060594	128567586	4068601	SRX1950211	SRS1564972	SRA440585	GEO	Reproductive Biology, Biology, Utrecht University	1	0.8315	0.27748	0.66985	0.56656	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-07-14	Adult	Adult	Gonad	Reproductive System
41190	41190	SRR3923674	SRX1950211	SRS1564972	SRP078537	PRJNA329141	Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis	GSE84436	Transcriptome Analysis	Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.		pubmed:27566230		Trilostane 5	GSM2236112		source name:Testis\|tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	Trilostane 5	Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	GSM2236112	GSM2236112: Trilostane 5; Danio rerio; RNA Seq	GSM2236112		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2236112	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP078537			Seq22_H9PG8ADXX_CGGCTATG-GTACTGAC_L002_R1_001.fastq.gz	fastq	447723500.0	8954470.0	GSM2236112 r2	0:50	A:108647571;C:105645041;G:102638902;T:126784624;N:4007362	50		108647571	105645041	102638902	126784624	4007362	SRX1950211	SRS1564972	SRA440585	GEO	Reproductive Biology, Biology, Utrecht University	1	0.83099	0.27799	0.66967	0.56426	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-07-14	Adult	Adult	Gonad	Reproductive System
41191	41191	SRR3923671	SRX1950210	SRS1564971	SRP078537	PRJNA329141	Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis	GSE84436	Transcriptome Analysis	Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.		pubmed:27566230		Trilostane 4	GSM2236111		source name:Testis\|tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	Trilostane 4	Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	GSM2236111	GSM2236111: Trilostane 4; Danio rerio; RNA Seq	GSM2236111		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2236111	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP078537			Seq12_H9PG8ADXX_ATTACTCG-GTACTGAC_L001_R1_001.fastq.gz	fastq	446491050.0	8929821.0	GSM2236111 r1	0:50	A:111285929;C:103826231;G:97244947;T:130091134;N:4042809	50		111285929	103826231	97244947	130091134	4042809	SRX1950210	SRS1564971	SRA440585	GEO	Reproductive Biology, Biology, Utrecht University	1	0.87061	0.31363	0.65111	0.55604	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-07-14	Adult	Adult	Gonad	Reproductive System
41192	41192	SRR3923672	SRX1950210	SRS1564971	SRP078537	PRJNA329141	Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis	GSE84436	Transcriptome Analysis	Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.		pubmed:27566230		Trilostane 4	GSM2236111		source name:Testis\|tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	Trilostane 4	Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	GSM2236111	GSM2236111: Trilostane 4; Danio rerio; RNA Seq	GSM2236111		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2236111	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP078537			Seq12_H9PG8ADXX_ATTACTCG-GTACTGAC_L002_R1_001.fastq.gz	fastq	445907350.0	8918147.0	GSM2236111 r2	0:50	A:111197446;C:103593829;G:97120345;T:129958338;N:4037392	50		111197446	103593829	97120345	129958338	4037392	SRX1950210	SRS1564971	SRA440585	GEO	Reproductive Biology, Biology, Utrecht University	1	0.86953	0.31237	0.65206	0.54599	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-07-14	Adult	Adult	Gonad	Reproductive System
41193	41193	SRR3923669	SRX1950209	SRS1564970	SRP078537	PRJNA329141	Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis	GSE84436	Transcriptome Analysis	Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.		pubmed:27566230		Trilostane 3	GSM2236110		source name:Testis\|tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	Trilostane 3	Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	GSM2236110	GSM2236110: Trilostane 3; Danio rerio; RNA Seq	GSM2236110		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2236110	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP078537			Seq10_H9PG8ADXX_AGCGATAG-CAGGACGT_L001_R1_001.fastq.gz	fastq	521947750.0	10438955.0	GSM2236110 r1	0:50	A:129320589;C:122268528;G:110282626;T:155469988;N:4606019	50		129320589	122268528	110282626	155469988	4606019	SRX1950209	SRS1564970	SRA440585	GEO	Reproductive Biology, Biology, Utrecht University	1	0.89087	0.3421	0.67123	0.59545	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-07-14	Adult	Adult	Gonad	Reproductive System
41194	41194	SRR3923670	SRX1950209	SRS1564970	SRP078537	PRJNA329141	Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis	GSE84436	Transcriptome Analysis	Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.		pubmed:27566230		Trilostane 3	GSM2236110		source name:Testis\|tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	Trilostane 3	Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	GSM2236110	GSM2236110: Trilostane 3; Danio rerio; RNA Seq	GSM2236110		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2236110	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP078537			Seq10_H9PG8ADXX_AGCGATAG-CAGGACGT_L002_R1_001.fastq.gz	fastq	516602850.0	10332057.0	GSM2236110 r2	0:50	A:128042316;C:121000293;G:109144625;T:153860728;N:4554888	50		128042316	121000293	109144625	153860728	4554888	SRX1950209	SRS1564970	SRA440585	GEO	Reproductive Biology, Biology, Utrecht University	1	0.89032	0.34188	0.67397	0.59669	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-07-14	Adult	Adult	Gonad	Reproductive System
41195	41195	SRR3923667	SRX1950208	SRS1564969	SRP078537	PRJNA329141	Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis	GSE84436	Transcriptome Analysis	Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.		pubmed:27566230		Trilostane 2	GSM2236109		source name:Testis\|tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	Trilostane 2	Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	GSM2236109	GSM2236109: Trilostane 2; Danio rerio; RNA Seq	GSM2236109		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2236109	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP078537			Seq5_H9PG8ADXX_GAATTCGT-CAGGACGT_L001_R1_001.fastq.gz	fastq	623611800.0	12472236.0	GSM2236109 r1	0:50	A:158989142;C:142414377;G:130317763;T:186223237;N:5667281	50		158989142	142414377	130317763	186223237	5667281	SRX1950208	SRS1564969	SRA440585	GEO	Reproductive Biology, Biology, Utrecht University	1	0.87898	0.32511	0.64934	0.46995	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-07-14	Adult	Adult	Gonad	Reproductive System
41196	41196	SRR3923668	SRX1950208	SRS1564969	SRP078537	PRJNA329141	Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis	GSE84436	Transcriptome Analysis	Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.		pubmed:27566230		Trilostane 2	GSM2236109		source name:Testis\|tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	Trilostane 2	Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	GSM2236109	GSM2236109: Trilostane 2; Danio rerio; RNA Seq	GSM2236109		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2236109	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP078537			Seq5_H9PG8ADXX_GAATTCGT-CAGGACGT_L002_R1_001.fastq.gz	fastq	625185750.0	12503715.0	GSM2236109 r2	0:50	A:159471869;C:142727575;G:130621469;T:186687783;N:5677054	50		159471869	142727575	130621469	186687783	5677054	SRX1950208	SRS1564969	SRA440585	GEO	Reproductive Biology, Biology, Utrecht University	1	0.8789	0.32679	0.65285	0.47033	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-07-14	Adult	Adult	Gonad	Reproductive System
41197	41197	SRR3923665	SRX1950207	SRS1564968	SRP078537	PRJNA329141	Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis	GSE84436	Transcriptome Analysis	Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.		pubmed:27566230		Trilostane 1	GSM2236108		source name:Testis\|tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	Trilostane 1	Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	GSM2236108	GSM2236108: Trilostane 1; Danio rerio; RNA Seq	GSM2236108		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2236108	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP078537			Seq2_H9PG8ADXX_TCCGGAGA-CAGGACGT_L001_R1_001.fastq.gz	fastq	437247150.0	8744943.0	GSM2236108 r1	0:50	A:96525256;C:120572709;G:101663845;T:115083503;N:3401837	50		96525256	120572709	101663845	115083503	3401837	SRX1950207	SRS1564968	SRA440585	GEO	Reproductive Biology, Biology, Utrecht University	1	0.92907	0.28985	0.7189	0.66088	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-07-14	Adult	Adult	Gonad	Reproductive System
41198	41198	SRR3923666	SRX1950207	SRS1564968	SRP078537	PRJNA329141	Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis	GSE84436	Transcriptome Analysis	Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane.		pubmed:27566230		Trilostane 1	GSM2236108		source name:Testis\|tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	Trilostane 1	Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample.	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		tissue:testis\|age:Adult\|genotype:Wild type\|incubation:48 hours	GSM2236108	GSM2236108: Trilostane 1; Danio rerio; RNA Seq	GSM2236108		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2236108	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP078537			Seq2_H9PG8ADXX_TCCGGAGA-CAGGACGT_L002_R1_001.fastq.gz	fastq	438228650.0	8764573.0	GSM2236108 r2	0:50	A:96748886;C:120843515;G:101940166;T:115290259;N:3405824	50		96748886	120843515	101940166	115290259	3405824	SRX1950207	SRS1564968	SRA440585	GEO	Reproductive Biology, Biology, Utrecht University	1	0.92905	0.29162	0.72214	0.64838	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-07-14	Adult	Adult	Gonad	Reproductive System
41338	41338	SRR4243173	SRX2164188	SRS1692133	SRP089896	PRJNA343041	Antagonistic regulation of spermatogonial differentiation in zebrafish Danio rerio by Igf3 and Amh	GSE86944	Transcriptome Analysis	Fsh mediated regulation of zebrafish spermatogenesis includes modulating the expression of testicular growth factors. Here we study if and how two Sertoli cell derived Fsh responsive growth factors anti Müllerian hormone Amh; inhibiting steroidogenesis and germ cell differentiation and insulin like growth factor 3 Igf3; stimulating germ cell differentiation cooperate in regulating spermatogonial development. In dose response and time course experiments with primary testis tissue cultures Fsh upregulated igf3 transcript levels and down regulated amh transcript levels; igf3 transcript levels were more rapidly up regulated and responded to lower Fsh concentrations than were required to decrease amh mRNA levels. Quantification of immunoreactive Amh and Igf3 on testis sections showed that Fsh increased slightly Igf3 staining but decreased clearly Amh staining. Studying the direct interaction of the two growth factors showed that Amh compromised Igf3 stimulated proliferation of type A both undifferentiated [Aund] and differentiating [Adiff] spermatogonia. Also the proliferation of those Sertoli cells associated with Aund spermatogonia was reduced by Amh. To gain more insight into how Amh inhibits germ cell development we examined Amh induced changes in testicular gene expression by RNA sequencing. The majority 69% of the differentially expressed genes was down regulated by Amh including several stimulators of spermatogenesis such as igf3 and steroidogenesis related genes. At the same time Amh increased the expression of inhibitory signals such as inha and id3 or facilitated prostaglandin E2 PGE2 signaling. Evaluating one of the potentially inhibitory signals we indeed found in tissue culture experiments that PGE2 promoted the accumulation of Aund at the expense of Adiff and B spermatogonia. Our data suggest that an important aspect of Fsh bioactivity in stimulating spermatogenesis is implemented by restricting the different inhibitory effects of Amh and by counterbalancing them with stimulatory signals such…		pubmed:28645700		11KT+Amh 5	GSM2310627		tissue:Testis\|age:Adult\|genotype:Wild type\|incubation:3 days\|treatment:Amh	11KT+Amh 5	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|incubation:3 days\|treatment:Amh	GSM2310627	GSM2310627: 11KT+Amh 5; Danio rerio; RNA Seq	GSM2310627		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2310627	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP089896			IL-14-08-16_GAGTGG_L001_R1_001.fastq.gz	fastq	1170392472.0	22948872.0	GSM2310627 r1	0:51	A:321032122;C:268515709;G:261725129;T:318830744;N:288768	51		321032122	268515709	261725129	318830744	288768	SRX2164188	SRS1692133	SRA471529	GEO	Reproductive Biology, Biology, Utrecht University	1	0.91255	0.11667	0.65137	0.50826	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-09-14	Adult	Adult	Gonad	Reproductive System
41339	41339	SRR4243172	SRX2164187	SRS1692132	SRP089896	PRJNA343041	Antagonistic regulation of spermatogonial differentiation in zebrafish Danio rerio by Igf3 and Amh	GSE86944	Transcriptome Analysis	Fsh mediated regulation of zebrafish spermatogenesis includes modulating the expression of testicular growth factors. Here we study if and how two Sertoli cell derived Fsh responsive growth factors anti Müllerian hormone Amh; inhibiting steroidogenesis and germ cell differentiation and insulin like growth factor 3 Igf3; stimulating germ cell differentiation cooperate in regulating spermatogonial development. In dose response and time course experiments with primary testis tissue cultures Fsh upregulated igf3 transcript levels and down regulated amh transcript levels; igf3 transcript levels were more rapidly up regulated and responded to lower Fsh concentrations than were required to decrease amh mRNA levels. Quantification of immunoreactive Amh and Igf3 on testis sections showed that Fsh increased slightly Igf3 staining but decreased clearly Amh staining. Studying the direct interaction of the two growth factors showed that Amh compromised Igf3 stimulated proliferation of type A both undifferentiated [Aund] and differentiating [Adiff] spermatogonia. Also the proliferation of those Sertoli cells associated with Aund spermatogonia was reduced by Amh. To gain more insight into how Amh inhibits germ cell development we examined Amh induced changes in testicular gene expression by RNA sequencing. The majority 69% of the differentially expressed genes was down regulated by Amh including several stimulators of spermatogenesis such as igf3 and steroidogenesis related genes. At the same time Amh increased the expression of inhibitory signals such as inha and id3 or facilitated prostaglandin E2 PGE2 signaling. Evaluating one of the potentially inhibitory signals we indeed found in tissue culture experiments that PGE2 promoted the accumulation of Aund at the expense of Adiff and B spermatogonia. Our data suggest that an important aspect of Fsh bioactivity in stimulating spermatogenesis is implemented by restricting the different inhibitory effects of Amh and by counterbalancing them with stimulatory signals such…		pubmed:28645700		11KT+Amh 4	GSM2310626		tissue:Testis\|age:Adult\|genotype:Wild type\|incubation:3 days\|treatment:Amh	11KT+Amh 4	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|incubation:3 days\|treatment:Amh	GSM2310626	GSM2310626: 11KT+Amh 4; Danio rerio; RNA Seq	GSM2310626		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2310626	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP089896			IL-14-08-15_CGTACG_L001_R1_001.fastq.gz	fastq	1020609348.0	20011948.0	GSM2310626 r1	0:51	A:280659283;C:233389387;G:227016796;T:279291132;N:252750	51		280659283	233389387	227016796	279291132	252750	SRX2164187	SRS1692132	SRA471529	GEO	Reproductive Biology, Biology, Utrecht University	1	0.91619	0.10708	0.66125	0.51479	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-09-14	Adult	Adult	Gonad	Reproductive System
41340	41340	SRR4243171	SRX2164186	SRS1692131	SRP089896	PRJNA343041	Antagonistic regulation of spermatogonial differentiation in zebrafish Danio rerio by Igf3 and Amh	GSE86944	Transcriptome Analysis	Fsh mediated regulation of zebrafish spermatogenesis includes modulating the expression of testicular growth factors. Here we study if and how two Sertoli cell derived Fsh responsive growth factors anti Müllerian hormone Amh; inhibiting steroidogenesis and germ cell differentiation and insulin like growth factor 3 Igf3; stimulating germ cell differentiation cooperate in regulating spermatogonial development. In dose response and time course experiments with primary testis tissue cultures Fsh upregulated igf3 transcript levels and down regulated amh transcript levels; igf3 transcript levels were more rapidly up regulated and responded to lower Fsh concentrations than were required to decrease amh mRNA levels. Quantification of immunoreactive Amh and Igf3 on testis sections showed that Fsh increased slightly Igf3 staining but decreased clearly Amh staining. Studying the direct interaction of the two growth factors showed that Amh compromised Igf3 stimulated proliferation of type A both undifferentiated [Aund] and differentiating [Adiff] spermatogonia. Also the proliferation of those Sertoli cells associated with Aund spermatogonia was reduced by Amh. To gain more insight into how Amh inhibits germ cell development we examined Amh induced changes in testicular gene expression by RNA sequencing. The majority 69% of the differentially expressed genes was down regulated by Amh including several stimulators of spermatogenesis such as igf3 and steroidogenesis related genes. At the same time Amh increased the expression of inhibitory signals such as inha and id3 or facilitated prostaglandin E2 PGE2 signaling. Evaluating one of the potentially inhibitory signals we indeed found in tissue culture experiments that PGE2 promoted the accumulation of Aund at the expense of Adiff and B spermatogonia. Our data suggest that an important aspect of Fsh bioactivity in stimulating spermatogenesis is implemented by restricting the different inhibitory effects of Amh and by counterbalancing them with stimulatory signals such…		pubmed:28645700		11KT+Amh 3	GSM2310625		tissue:Testis\|age:Adult\|genotype:Wild type\|incubation:3 days\|treatment:Amh	11KT+Amh 3	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|incubation:3 days\|treatment:Amh	GSM2310625	GSM2310625: 11KT+Amh 3; Danio rerio; RNA Seq	GSM2310625		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2310625	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP089896			IL-14-08-12_GTTTCG_L001_R1_001.fastq.gz	fastq	903981069.0	17725119.0	GSM2310625 r1	0:51	A:248045770;C:207394369;G:201577494;T:246739594;N:223842	51		248045770	207394369	201577494	246739594	223842	SRX2164186	SRS1692131	SRA471529	GEO	Reproductive Biology, Biology, Utrecht University	1	0.9133	0.11386	0.66782	0.50462	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-09-14	Adult	Adult	Gonad	Reproductive System
41341	41341	SRR4243170	SRX2164185	SRS1692130	SRP089896	PRJNA343041	Antagonistic regulation of spermatogonial differentiation in zebrafish Danio rerio by Igf3 and Amh	GSE86944	Transcriptome Analysis	Fsh mediated regulation of zebrafish spermatogenesis includes modulating the expression of testicular growth factors. Here we study if and how two Sertoli cell derived Fsh responsive growth factors anti Müllerian hormone Amh; inhibiting steroidogenesis and germ cell differentiation and insulin like growth factor 3 Igf3; stimulating germ cell differentiation cooperate in regulating spermatogonial development. In dose response and time course experiments with primary testis tissue cultures Fsh upregulated igf3 transcript levels and down regulated amh transcript levels; igf3 transcript levels were more rapidly up regulated and responded to lower Fsh concentrations than were required to decrease amh mRNA levels. Quantification of immunoreactive Amh and Igf3 on testis sections showed that Fsh increased slightly Igf3 staining but decreased clearly Amh staining. Studying the direct interaction of the two growth factors showed that Amh compromised Igf3 stimulated proliferation of type A both undifferentiated [Aund] and differentiating [Adiff] spermatogonia. Also the proliferation of those Sertoli cells associated with Aund spermatogonia was reduced by Amh. To gain more insight into how Amh inhibits germ cell development we examined Amh induced changes in testicular gene expression by RNA sequencing. The majority 69% of the differentially expressed genes was down regulated by Amh including several stimulators of spermatogenesis such as igf3 and steroidogenesis related genes. At the same time Amh increased the expression of inhibitory signals such as inha and id3 or facilitated prostaglandin E2 PGE2 signaling. Evaluating one of the potentially inhibitory signals we indeed found in tissue culture experiments that PGE2 promoted the accumulation of Aund at the expense of Adiff and B spermatogonia. Our data suggest that an important aspect of Fsh bioactivity in stimulating spermatogenesis is implemented by restricting the different inhibitory effects of Amh and by counterbalancing them with stimulatory signals such…		pubmed:28645700		11KT+Amh 2	GSM2310624		tissue:Testis\|age:Adult\|genotype:Wild type\|incubation:3 days\|treatment:Amh	11KT+Amh 2	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|incubation:3 days\|treatment:Amh	GSM2310624	GSM2310624: 11KT+Amh 2; Danio rerio; RNA Seq	GSM2310624		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2310624	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP089896			IL-14-08-11_GTGGCC_L001_R1_001.fastq.gz	fastq	818454171.0	16048121.0	GSM2310624 r1	0:51	A:224174167;C:188064997;G:183412696;T:222602796;N:199515	51		224174167	188064997	183412696	222602796	199515	SRX2164185	SRS1692130	SRA471529	GEO	Reproductive Biology, Biology, Utrecht University	1	0.91371	0.11249	0.66074	0.52081	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-09-14	Adult	Adult	Gonad	Reproductive System
41342	41342	SRR4243169	SRX2164184	SRS1692129	SRP089896	PRJNA343041	Antagonistic regulation of spermatogonial differentiation in zebrafish Danio rerio by Igf3 and Amh	GSE86944	Transcriptome Analysis	Fsh mediated regulation of zebrafish spermatogenesis includes modulating the expression of testicular growth factors. Here we study if and how two Sertoli cell derived Fsh responsive growth factors anti Müllerian hormone Amh; inhibiting steroidogenesis and germ cell differentiation and insulin like growth factor 3 Igf3; stimulating germ cell differentiation cooperate in regulating spermatogonial development. In dose response and time course experiments with primary testis tissue cultures Fsh upregulated igf3 transcript levels and down regulated amh transcript levels; igf3 transcript levels were more rapidly up regulated and responded to lower Fsh concentrations than were required to decrease amh mRNA levels. Quantification of immunoreactive Amh and Igf3 on testis sections showed that Fsh increased slightly Igf3 staining but decreased clearly Amh staining. Studying the direct interaction of the two growth factors showed that Amh compromised Igf3 stimulated proliferation of type A both undifferentiated [Aund] and differentiating [Adiff] spermatogonia. Also the proliferation of those Sertoli cells associated with Aund spermatogonia was reduced by Amh. To gain more insight into how Amh inhibits germ cell development we examined Amh induced changes in testicular gene expression by RNA sequencing. The majority 69% of the differentially expressed genes was down regulated by Amh including several stimulators of spermatogenesis such as igf3 and steroidogenesis related genes. At the same time Amh increased the expression of inhibitory signals such as inha and id3 or facilitated prostaglandin E2 PGE2 signaling. Evaluating one of the potentially inhibitory signals we indeed found in tissue culture experiments that PGE2 promoted the accumulation of Aund at the expense of Adiff and B spermatogonia. Our data suggest that an important aspect of Fsh bioactivity in stimulating spermatogenesis is implemented by restricting the different inhibitory effects of Amh and by counterbalancing them with stimulatory signals such…		pubmed:28645700		11KT+Amh 1	GSM2310623		tissue:Testis\|age:Adult\|genotype:Wild type\|incubation:3 days\|treatment:Amh	11KT+Amh 1	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|incubation:3 days\|treatment:Amh	GSM2310623	GSM2310623: 11KT+Amh 1; Danio rerio; RNA Seq	GSM2310623		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2310623	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP089896			IL-14-08-9_GGCTAC_L001_R1_001.fastq.gz	fastq	1030828830.0	20212330.0	GSM2310623 r1	0:51	A:282285319;C:237657119;G:230237273;T:280396581;N:252538	51		282285319	237657119	230237273	280396581	252538	SRX2164184	SRS1692129	SRA471529	GEO	Reproductive Biology, Biology, Utrecht University	1	0.90885	0.11549	0.65869	0.49547	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-09-14	Adult	Adult	Gonad	Reproductive System
41343	41343	SRR4243168	SRX2164183	SRS1692128	SRP089896	PRJNA343041	Antagonistic regulation of spermatogonial differentiation in zebrafish Danio rerio by Igf3 and Amh	GSE86944	Transcriptome Analysis	Fsh mediated regulation of zebrafish spermatogenesis includes modulating the expression of testicular growth factors. Here we study if and how two Sertoli cell derived Fsh responsive growth factors anti Müllerian hormone Amh; inhibiting steroidogenesis and germ cell differentiation and insulin like growth factor 3 Igf3; stimulating germ cell differentiation cooperate in regulating spermatogonial development. In dose response and time course experiments with primary testis tissue cultures Fsh upregulated igf3 transcript levels and down regulated amh transcript levels; igf3 transcript levels were more rapidly up regulated and responded to lower Fsh concentrations than were required to decrease amh mRNA levels. Quantification of immunoreactive Amh and Igf3 on testis sections showed that Fsh increased slightly Igf3 staining but decreased clearly Amh staining. Studying the direct interaction of the two growth factors showed that Amh compromised Igf3 stimulated proliferation of type A both undifferentiated [Aund] and differentiating [Adiff] spermatogonia. Also the proliferation of those Sertoli cells associated with Aund spermatogonia was reduced by Amh. To gain more insight into how Amh inhibits germ cell development we examined Amh induced changes in testicular gene expression by RNA sequencing. The majority 69% of the differentially expressed genes was down regulated by Amh including several stimulators of spermatogenesis such as igf3 and steroidogenesis related genes. At the same time Amh increased the expression of inhibitory signals such as inha and id3 or facilitated prostaglandin E2 PGE2 signaling. Evaluating one of the potentially inhibitory signals we indeed found in tissue culture experiments that PGE2 promoted the accumulation of Aund at the expense of Adiff and B spermatogonia. Our data suggest that an important aspect of Fsh bioactivity in stimulating spermatogenesis is implemented by restricting the different inhibitory effects of Amh and by counterbalancing them with stimulatory signals such…		pubmed:28645700		11KT 5	GSM2310622		tissue:Testis\|age:Adult\|genotype:Wild type\|incubation:3 days\|treatment:control	11KT 5	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|incubation:3 days\|treatment:control	GSM2310622	GSM2310622: 11KT 5; Danio rerio; RNA Seq	GSM2310622		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2310622	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP089896			IL-14-08-8_TAGCTT_L001_R1_001.fastq.gz	fastq	906867771.0	17781721.0	GSM2310622 r1	0:51	A:248681526;C:208321293;G:202986876;T:246659593;N:218483	51		248681526	208321293	202986876	246659593	218483	SRX2164183	SRS1692128	SRA471529	GEO	Reproductive Biology, Biology, Utrecht University	1	0.91216	0.11605	0.65533	0.50523	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-09-14	Adult	Adult	Gonad	Reproductive System
41344	41344	SRR4243167	SRX2164182	SRS1692127	SRP089896	PRJNA343041	Antagonistic regulation of spermatogonial differentiation in zebrafish Danio rerio by Igf3 and Amh	GSE86944	Transcriptome Analysis	Fsh mediated regulation of zebrafish spermatogenesis includes modulating the expression of testicular growth factors. Here we study if and how two Sertoli cell derived Fsh responsive growth factors anti Müllerian hormone Amh; inhibiting steroidogenesis and germ cell differentiation and insulin like growth factor 3 Igf3; stimulating germ cell differentiation cooperate in regulating spermatogonial development. In dose response and time course experiments with primary testis tissue cultures Fsh upregulated igf3 transcript levels and down regulated amh transcript levels; igf3 transcript levels were more rapidly up regulated and responded to lower Fsh concentrations than were required to decrease amh mRNA levels. Quantification of immunoreactive Amh and Igf3 on testis sections showed that Fsh increased slightly Igf3 staining but decreased clearly Amh staining. Studying the direct interaction of the two growth factors showed that Amh compromised Igf3 stimulated proliferation of type A both undifferentiated [Aund] and differentiating [Adiff] spermatogonia. Also the proliferation of those Sertoli cells associated with Aund spermatogonia was reduced by Amh. To gain more insight into how Amh inhibits germ cell development we examined Amh induced changes in testicular gene expression by RNA sequencing. The majority 69% of the differentially expressed genes was down regulated by Amh including several stimulators of spermatogenesis such as igf3 and steroidogenesis related genes. At the same time Amh increased the expression of inhibitory signals such as inha and id3 or facilitated prostaglandin E2 PGE2 signaling. Evaluating one of the potentially inhibitory signals we indeed found in tissue culture experiments that PGE2 promoted the accumulation of Aund at the expense of Adiff and B spermatogonia. Our data suggest that an important aspect of Fsh bioactivity in stimulating spermatogenesis is implemented by restricting the different inhibitory effects of Amh and by counterbalancing them with stimulatory signals such…		pubmed:28645700		11KT 4	GSM2310621		tissue:Testis\|age:Adult\|genotype:Wild type\|incubation:3 days\|treatment:control	11KT 4	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|incubation:3 days\|treatment:control	GSM2310621	GSM2310621: 11KT 4; Danio rerio; RNA Seq	GSM2310621		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2310621	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP089896			IL-14-08-7_GATCAG_L001_R1_001.fastq.gz	fastq	810915249.0	15900299.0	GSM2310621 r1	0:51	A:223051661;C:185259732;G:180275369;T:222124161;N:204326	51		223051661	185259732	180275369	222124161	204326	SRX2164182	SRS1692127	SRA471529	GEO	Reproductive Biology, Biology, Utrecht University	1	0.91741	0.11127	0.65729	0.52493	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-09-14	Adult	Adult	Gonad	Reproductive System
41345	41345	SRR4243166	SRX2164181	SRS1692126	SRP089896	PRJNA343041	Antagonistic regulation of spermatogonial differentiation in zebrafish Danio rerio by Igf3 and Amh	GSE86944	Transcriptome Analysis	Fsh mediated regulation of zebrafish spermatogenesis includes modulating the expression of testicular growth factors. Here we study if and how two Sertoli cell derived Fsh responsive growth factors anti Müllerian hormone Amh; inhibiting steroidogenesis and germ cell differentiation and insulin like growth factor 3 Igf3; stimulating germ cell differentiation cooperate in regulating spermatogonial development. In dose response and time course experiments with primary testis tissue cultures Fsh upregulated igf3 transcript levels and down regulated amh transcript levels; igf3 transcript levels were more rapidly up regulated and responded to lower Fsh concentrations than were required to decrease amh mRNA levels. Quantification of immunoreactive Amh and Igf3 on testis sections showed that Fsh increased slightly Igf3 staining but decreased clearly Amh staining. Studying the direct interaction of the two growth factors showed that Amh compromised Igf3 stimulated proliferation of type A both undifferentiated [Aund] and differentiating [Adiff] spermatogonia. Also the proliferation of those Sertoli cells associated with Aund spermatogonia was reduced by Amh. To gain more insight into how Amh inhibits germ cell development we examined Amh induced changes in testicular gene expression by RNA sequencing. The majority 69% of the differentially expressed genes was down regulated by Amh including several stimulators of spermatogenesis such as igf3 and steroidogenesis related genes. At the same time Amh increased the expression of inhibitory signals such as inha and id3 or facilitated prostaglandin E2 PGE2 signaling. Evaluating one of the potentially inhibitory signals we indeed found in tissue culture experiments that PGE2 promoted the accumulation of Aund at the expense of Adiff and B spermatogonia. Our data suggest that an important aspect of Fsh bioactivity in stimulating spermatogenesis is implemented by restricting the different inhibitory effects of Amh and by counterbalancing them with stimulatory signals such…		pubmed:28645700		11KT 3	GSM2310620		tissue:Testis\|age:Adult\|genotype:Wild type\|incubation:3 days\|treatment:control	11KT 3	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|incubation:3 days\|treatment:control	GSM2310620	GSM2310620: 11KT 3; Danio rerio; RNA Seq	GSM2310620		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2310620	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP089896			IL-14-08-4_ACTTGA_L001_R1_001.fastq.gz	fastq	762603000.0	14953000.0	GSM2310620 r1	0:51	A:208388925;C:174982032;G:171459809;T:207583812;N:188422	51		208388925	174982032	171459809	207583812	188422	SRX2164181	SRS1692126	SRA471529	GEO	Reproductive Biology, Biology, Utrecht University	1	0.91126	0.12186	0.669	0.4979	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-09-14	Adult	Adult	Gonad	Reproductive System
41346	41346	SRR4243165	SRX2164180	SRS1692125	SRP089896	PRJNA343041	Antagonistic regulation of spermatogonial differentiation in zebrafish Danio rerio by Igf3 and Amh	GSE86944	Transcriptome Analysis	Fsh mediated regulation of zebrafish spermatogenesis includes modulating the expression of testicular growth factors. Here we study if and how two Sertoli cell derived Fsh responsive growth factors anti Müllerian hormone Amh; inhibiting steroidogenesis and germ cell differentiation and insulin like growth factor 3 Igf3; stimulating germ cell differentiation cooperate in regulating spermatogonial development. In dose response and time course experiments with primary testis tissue cultures Fsh upregulated igf3 transcript levels and down regulated amh transcript levels; igf3 transcript levels were more rapidly up regulated and responded to lower Fsh concentrations than were required to decrease amh mRNA levels. Quantification of immunoreactive Amh and Igf3 on testis sections showed that Fsh increased slightly Igf3 staining but decreased clearly Amh staining. Studying the direct interaction of the two growth factors showed that Amh compromised Igf3 stimulated proliferation of type A both undifferentiated [Aund] and differentiating [Adiff] spermatogonia. Also the proliferation of those Sertoli cells associated with Aund spermatogonia was reduced by Amh. To gain more insight into how Amh inhibits germ cell development we examined Amh induced changes in testicular gene expression by RNA sequencing. The majority 69% of the differentially expressed genes was down regulated by Amh including several stimulators of spermatogenesis such as igf3 and steroidogenesis related genes. At the same time Amh increased the expression of inhibitory signals such as inha and id3 or facilitated prostaglandin E2 PGE2 signaling. Evaluating one of the potentially inhibitory signals we indeed found in tissue culture experiments that PGE2 promoted the accumulation of Aund at the expense of Adiff and B spermatogonia. Our data suggest that an important aspect of Fsh bioactivity in stimulating spermatogenesis is implemented by restricting the different inhibitory effects of Amh and by counterbalancing them with stimulatory signals such…		pubmed:28645700		11KT 2	GSM2310619		tissue:Testis\|age:Adult\|genotype:Wild type\|incubation:3 days\|treatment:control	11KT 2	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|incubation:3 days\|treatment:control	GSM2310619	GSM2310619: 11KT 2; Danio rerio; RNA Seq	GSM2310619		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2310619	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP089896			IL-14-08-3_TTAGGC_L001_R1_001.fastq.gz	fastq	693008247.0	13588397.0	GSM2310619 r1	0:51	A:199282612;C:150789916;G:146878078;T:195891642;N:165999	51		199282612	150789916	146878078	195891642	165999	SRX2164180	SRS1692125	SRA471529	GEO	Reproductive Biology, Biology, Utrecht University	1	0.8977	0.16323	0.65695	0.52131	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-09-14	Adult	Adult	Gonad	Reproductive System
41347	41347	SRR4243164	SRX2164179	SRS1692124	SRP089896	PRJNA343041	Antagonistic regulation of spermatogonial differentiation in zebrafish Danio rerio by Igf3 and Amh	GSE86944	Transcriptome Analysis	Fsh mediated regulation of zebrafish spermatogenesis includes modulating the expression of testicular growth factors. Here we study if and how two Sertoli cell derived Fsh responsive growth factors anti Müllerian hormone Amh; inhibiting steroidogenesis and germ cell differentiation and insulin like growth factor 3 Igf3; stimulating germ cell differentiation cooperate in regulating spermatogonial development. In dose response and time course experiments with primary testis tissue cultures Fsh upregulated igf3 transcript levels and down regulated amh transcript levels; igf3 transcript levels were more rapidly up regulated and responded to lower Fsh concentrations than were required to decrease amh mRNA levels. Quantification of immunoreactive Amh and Igf3 on testis sections showed that Fsh increased slightly Igf3 staining but decreased clearly Amh staining. Studying the direct interaction of the two growth factors showed that Amh compromised Igf3 stimulated proliferation of type A both undifferentiated [Aund] and differentiating [Adiff] spermatogonia. Also the proliferation of those Sertoli cells associated with Aund spermatogonia was reduced by Amh. To gain more insight into how Amh inhibits germ cell development we examined Amh induced changes in testicular gene expression by RNA sequencing. The majority 69% of the differentially expressed genes was down regulated by Amh including several stimulators of spermatogenesis such as igf3 and steroidogenesis related genes. At the same time Amh increased the expression of inhibitory signals such as inha and id3 or facilitated prostaglandin E2 PGE2 signaling. Evaluating one of the potentially inhibitory signals we indeed found in tissue culture experiments that PGE2 promoted the accumulation of Aund at the expense of Adiff and B spermatogonia. Our data suggest that an important aspect of Fsh bioactivity in stimulating spermatogenesis is implemented by restricting the different inhibitory effects of Amh and by counterbalancing them with stimulatory signals such…		pubmed:28645700		11KT 1	GSM2310618		tissue:Testis\|age:Adult\|genotype:Wild type\|incubation:3 days\|treatment:control	11KT 1	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|incubation:3 days\|treatment:control	GSM2310618	GSM2310618: 11KT 1; Danio rerio; RNA Seq	GSM2310618		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions	GEO Accession:GSM2310618	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP089896			IL-14-08-1_ATCACG_L001_R1_001.fastq.gz	fastq	836727216.0	16406416.0	GSM2310618 r1	0:51	A:228522236;C:192582706;G:188473692;T:226939267;N:209315	51		228522236	192582706	188473692	226939267	209315	SRX2164179	SRS1692124	SRA471529	GEO	Reproductive Biology, Biology, Utrecht University	1	0.91111	0.11625	0.66249	0.50635	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2016-09-14	Adult	Adult	Gonad	Reproductive System
41847	41847	SRR5892569	SRX3058262	SRS2404198	SRP100178	PRJNA375788	'Placeholder' nucleosomes underlie germline to embryo DNA methylation reprogramming [RNA Seq]	GSE95031	Transcriptome Analysis	The function and retention/reprogramming of epigenetic marks during the germline to embryo transition is a key issue in developmental and cellular biology with relevance to stem cell programming and trans generational inheritance. In zebrafish DNAme patterns are programmed in transcriptionally quiescent early cleavage embryos; paternally inherited patterns are maintained whereas maternal patterns are reprogrammed to match the paternal pattern. Here we show that a 'placeholder' nucleosome containing the histone H2A variant H2A.ZFV and H3K4me1 occupies virtually all regions lacking DNAme in both sperm and cleavage embryos – residing at promoters encoding housekeeping and early embryonic transcription factors. Upon genome wide transcriptional onset genes with the Placeholder become either active H3K4me3 marked or silent H3K4me3/K27me3 marked bivalent. Importantly functional perturbation causing Placeholder loss confers DNAme acquisition whereas acquisition/expansion of Placeholder confers DNA hypomethylation and improper gene activation. Thus during transcriptionally quiescent stages gamete zygote cleavage an H2A.ZFV/H3K4me1 containing Placeholder nucleosome deters DNAme poising parental genes for either gene specific activation or facultative repression. Overall design: Transcript abundance was analyzed for zebrafish sperm and cleavage stage embryos that were either wild type or mutant for the anp32e gene.	parent bioproject:PRJNA375781	pubmed:29456083		Anp32e Null Sperm RNA Seq Rep2	GSM2730572		tissue:Sperm Stage\|developmental stage:Sperm Stage\|strain:NA\|injection:NA\|mutation:Anp32e Null	Anp32e Null Sperm RNA Seq Rep2	Reads were aligned to the Zv10 genome using Novoalign v2.8 Novocraft using the following options: o SAM r All 50 Sam files were then combined due to high correlation between technical and biological replicates. The Useq Pipeline was utilized Sam parsed using the SAMTranscriptomeParser followed by DefinedRegionDifferentialSeq which utilizes DeSeq2 to generate differential gene expression tables and FPKM values. Genome build: Zv10 Supplementary files format and content: RNASeq geneCount minimum10.xlsx: Excel file contains gene count table.	Sperm Stage		Embryos were lysed using Trizol with the addition of 2% SDS then homogenized using a 20G needle. Sample were then phenol extracted and the aqueous phase was added to a Qiagen RNA miniElute column for final purification. Illumina TruSeq Stranded RNA kit with Rib Zero Gold		developmental stage:Sperm Stage\|strain:NA\|injection:NA\|mutation:Anp32e Null	GSM2730572	GSM2730572: Anp32e Null Sperm RNA Seq Rep2; Danio rerio; RNA Seq	GSM2730572		1	Embryos were lysed using Trizol with the addition of 2% SDS then homogenized using a 20G needle. Sample were then phenol extracted and the aqueous phase was added to a Qiagen RNA miniElute column for final purification. Illumina TruSeq Stranded RNA kit with Rib Zero Gold	GEO Accession:GSM2730572	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP100178			Anp32e_Null_Sperm_RNA-Seq_Rep2.fastq.gz	fastq	2612583700.0	52251674.0	GSM2730572 r1	0:50	A:643932236;C:630114587;G:625850241;T:712599561;N:87075	50		643932236	630114587	625850241	712599561	87075	SRX3058262	SRS2404198	SRA538756	GEO	Huntsman Cancer Institute	1	0.91107	0.05039	0.76108	0.4698	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2017-08-03	Zygote	Embryo	Oocyte	Reproductive System
41848	41848	SRR5892568	SRX3058261	SRS2404197	SRP100178	PRJNA375788	'Placeholder' nucleosomes underlie germline to embryo DNA methylation reprogramming [RNA Seq]	GSE95031	Transcriptome Analysis	The function and retention/reprogramming of epigenetic marks during the germline to embryo transition is a key issue in developmental and cellular biology with relevance to stem cell programming and trans generational inheritance. In zebrafish DNAme patterns are programmed in transcriptionally quiescent early cleavage embryos; paternally inherited patterns are maintained whereas maternal patterns are reprogrammed to match the paternal pattern. Here we show that a 'placeholder' nucleosome containing the histone H2A variant H2A.ZFV and H3K4me1 occupies virtually all regions lacking DNAme in both sperm and cleavage embryos – residing at promoters encoding housekeeping and early embryonic transcription factors. Upon genome wide transcriptional onset genes with the Placeholder become either active H3K4me3 marked or silent H3K4me3/K27me3 marked bivalent. Importantly functional perturbation causing Placeholder loss confers DNAme acquisition whereas acquisition/expansion of Placeholder confers DNA hypomethylation and improper gene activation. Thus during transcriptionally quiescent stages gamete zygote cleavage an H2A.ZFV/H3K4me1 containing Placeholder nucleosome deters DNAme poising parental genes for either gene specific activation or facultative repression. Overall design: Transcript abundance was analyzed for zebrafish sperm and cleavage stage embryos that were either wild type or mutant for the anp32e gene.	parent bioproject:PRJNA375781	pubmed:29456083		Anp32e Null Sperm RNA Seq Rep1	GSM2730571		tissue:Sperm Stage\|developmental stage:Sperm Stage\|strain:NA\|injection:NA\|mutation:Anp32e Null	Anp32e Null Sperm RNA Seq Rep1	Reads were aligned to the Zv10 genome using Novoalign v2.8 Novocraft using the following options: o SAM r All 50 Sam files were then combined due to high correlation between technical and biological replicates. The Useq Pipeline was utilized Sam parsed using the SAMTranscriptomeParser followed by DefinedRegionDifferentialSeq which utilizes DeSeq2 to generate differential gene expression tables and FPKM values. Genome build: Zv10 Supplementary files format and content: RNASeq geneCount minimum10.xlsx: Excel file contains gene count table.	Sperm Stage		Embryos were lysed using Trizol with the addition of 2% SDS then homogenized using a 20G needle. Sample were then phenol extracted and the aqueous phase was added to a Qiagen RNA miniElute column for final purification. Illumina TruSeq Stranded RNA kit with Rib Zero Gold		developmental stage:Sperm Stage\|strain:NA\|injection:NA\|mutation:Anp32e Null	GSM2730571	GSM2730571: Anp32e Null Sperm RNA Seq Rep1; Danio rerio; RNA Seq	GSM2730571		1	Embryos were lysed using Trizol with the addition of 2% SDS then homogenized using a 20G needle. Sample were then phenol extracted and the aqueous phase was added to a Qiagen RNA miniElute column for final purification. Illumina TruSeq Stranded RNA kit with Rib Zero Gold	GEO Accession:GSM2730571	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP100178			Anp32e_Null_Sperm_RNA-Seq_Rep1.fastq.gz	fastq	3162821050.0	63256421.0	GSM2730571 r1	0:50	A:756571256;C:759039692;G:777010061;T:870095540;N:104501	50		756571256	759039692	777010061	870095540	104501	SRX3058261	SRS2404197	SRA538756	GEO	Huntsman Cancer Institute	1	0.91819	0.04312	0.76307	0.45972	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2017-08-03	Zygote	Embryo	Oocyte	Reproductive System
48337	48337	SRR7762357	SRX4617974	SRS3720953	SRP149356	PRJNA473799	Widespread enhancer dememorization and promoter priming during parental to zygotic transition	GSE114954	Other	The epigenome plays critical roles in controlling gene expression and development. However how the parental epigenomes transit to the zygotic epigenome in early development remains elusive. Here we show parental to zygotic transition in zebrafish involves extensive erasure of parental epigenetic memory starting by methylating gametic enhancers. Surprisingly this occurs even prior to fertilization for sperm. Both parental enhancers lose histone marks by the 4 cell stage and zygotic enhancers are not activated until around zygotic genome activation ZGA. By contrast many promoters remain hypomethylated and unexpectedly acquire de novo histone acetylation as early as at the 4 cell stage. They then resolve into either activated or repressed promoters upon ZGA. Maternal depletion of histone acetyltransferases results in aberrant ZGA and early embryonic lethality. Finally such reprogramming is largely driven by maternal factors with zygotic products contributing to embryonic enhancer activation. Thus these data revealed widespread enhancer dememorization and promoter priming during parental to zygotic transition. Overall design: By employing STAR ChIP seq and RNA seq we systematically examined the genome wide presence of H3K4me3 H3K27ac H3K27me3 and H3K36me3 in sperm oocyte 4 cell 256 cell and dome stage embryos.		pubmed:30444999		oocyte IV RNA seq	GSM3359500		tissue:oocyte\|developmental stage:stage IV\|cell type:metaphase I oocyte\|strain:Tu	oocyte IV RNA seq	RNA seq data were firstly processed using Trim Galore! with default parameters to trim the adapter containing and low quality reads.The filtered data were then mapped to the zebrafish reference genome danRer7 by STAR version: STAR 2.5.3a modified with following parameters: outSAMstrandField intronMotif outSAMattributes All outSAMunmapped Within outSAMattrIHstart 0 outWigStrand Stranded outFilterMultimapNmax 20 twopassMode Basic. All STAR ChIP seq reads were aligned to the zebrafish reference genome danRer7 using Bowtie2 version 2.2.2 Langmead and Salzberg 2012 with the parameters –t –q –N 1 –L 25. All unmapped reads non uniquely mapped reads and PCR duplicates were removed. For downstream analysis the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced RPKM. All STEM seq datasets were mapped to the danRer7 reference genome by Bismark Krueger and Andrews 2011. Reads were trimmed with cutadaptor Martin 2011 using parameters: minimum length 20 pair filter=any. Alignments were performed with the following parameters: N 1 X 600 score min L 0 0.6. Multi mapped reads and PCR duplicates were removed. bismark methylation extractor was used to calculate the DNA methylation level Genome build: danRer7 Supplementary files format and content: Bigwig for ChIP seq and RNA seq tracks gene expression table for RNA seq data	oocyte	The ovaries of adult female were isolated and transferred into specific buffer 5.4 mM KCl 136.8 mM NaCl 4.2 mM NaHCO3 0.44 mM KH2PO4 0.25 mM Na2HPO4 and 0.5% wt/vol BSA. Then stage I V oocytes were separated from the ovary with tweezers under microscope according to their morphology and the surrounding follicle cells were detached gently as much as possible.	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols 5 ug RNA was DNase I Fermentas Cat # EN0521 treated at 37C for 1 h. RNA was then purified using AMPure beads. Poly A tailed mRNA was collected using DynabeadsTM mRNA purification kit Invitrogen Cat # 61006. Purified RNA was fragmented with RNA Frag. Buffer NEB Cat # E6186A at 95C for 5 min. Reaction was stopped and RNA was purified by AMPure beads. First stand cDNA was synthesized with a commercial kit using both oligo dT and random primers Invitrogen Cat # 18080 051. Second strand cDNA was synthesized with second strand synthesis buffer Invitrogen Cat # 10812014 MgCl2 DTT dNTP dUTP RNase H Fermentas Cat # EN0202 E. coli DNA ligase NEB Cat # M0205S and DNA polymerase I NEB Cat # M0209S. DNA was purified post 2 hrs incubation on thermomixer at 16C. Synthesized cDNA was subjected to library preparation. DNA was end repaired adenylated and ligated to TruSeq sequencing adaptors. Libraries were then treated with UDG AMPErase Cat # N808 0096 at 37C for 1 hour followed by DNA amplification using Phusion HF DNA polymerase NEB Cat # M0530L. The amplified DNA was size selected using AMPure Beads for 200 500 bp DNA fragments.	The wild type Tu female strain were raised as standard protocol.	developmental stage:stage IV\|cell type:metaphase I oocyte\|strain:Tu	GSM3359500	GSM3359500: oocyte IV RNA seq; Danio rerio; RNA Seq	GSM3359500		1	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols 5 ug RNA was DNase I Fermentas Cat # EN0521 treated at 37C for 1 h. RNA was then purified using AMPure beads. Poly A tailed mRNA was collected using DynabeadsTM mRNA purification kit Invitrogen Cat # 61006. Purified RNA was fragmented with RNA Frag. Buffer NEB Cat # E6186A at 95C for 5 min. Reaction was stopped and RNA was purified by AMPure beads. First stand cDNA was synthesized with a commercial kit using both oligo dT and random primers Invitrogen Cat # 18080 051. Second strand cDNA was synthesized with second strand synthesis buffer Invitrogen Cat # 10812014 MgCl2 DTT dNTP dUTP RNase H Fermentas Cat # EN0202 E. coli DNA ligase NEB Cat # M0205S and DNA polymerase I NEB Cat # M0209S. DNA was purified post 2 hrs incubation on thermomixer at 16C. Synthesized cDNA was subjected to library preparation. DNA was end repaired adenylated and ligated to TruSeq sequencing adaptors. Libraries were then treated with UDG AMPErase Cat # N808 0096 at 37C for 1 hour followed by DNA amplification using Phusion HF DNA polymerase NEB Cat # M0530L. The amplified DNA was size selected using AMPure Beads for 200 500 bp DNA fragments.	GEO Accession:GSM3359500	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 1500		SRP149356			oocyte_IV_RNA_seq_r1.fq.gz	fastq	636442625.0	12988625.0	GSM3359500 r1	0:49 1:0	A:159884635;C:154136157;G:161233162;T:161078773;N:109898	49	0	159884635	154136157	161233162	161078773	109898	SRX4617974	SRS3720953	SRA712563	GEO	Tsinghua University	1	0.94159	0.02577	0.79933	0.46881	49	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2018-08-28	Zygote	Embryo	Oocyte	Reproductive System
48338	48338	SRR7762356	SRX4617973	SRS3720954	SRP149356	PRJNA473799	Widespread enhancer dememorization and promoter priming during parental to zygotic transition	GSE114954	Other	The epigenome plays critical roles in controlling gene expression and development. However how the parental epigenomes transit to the zygotic epigenome in early development remains elusive. Here we show parental to zygotic transition in zebrafish involves extensive erasure of parental epigenetic memory starting by methylating gametic enhancers. Surprisingly this occurs even prior to fertilization for sperm. Both parental enhancers lose histone marks by the 4 cell stage and zygotic enhancers are not activated until around zygotic genome activation ZGA. By contrast many promoters remain hypomethylated and unexpectedly acquire de novo histone acetylation as early as at the 4 cell stage. They then resolve into either activated or repressed promoters upon ZGA. Maternal depletion of histone acetyltransferases results in aberrant ZGA and early embryonic lethality. Finally such reprogramming is largely driven by maternal factors with zygotic products contributing to embryonic enhancer activation. Thus these data revealed widespread enhancer dememorization and promoter priming during parental to zygotic transition. Overall design: By employing STAR ChIP seq and RNA seq we systematically examined the genome wide presence of H3K4me3 H3K27ac H3K27me3 and H3K36me3 in sperm oocyte 4 cell 256 cell and dome stage embryos.		pubmed:30444999		oocyte III RNA seq	GSM3359499		tissue:oocyte\|developmental stage:stage III\|cell type:prophase I oocyte\|strain:Tu	oocyte III RNA seq	RNA seq data were firstly processed using Trim Galore! with default parameters to trim the adapter containing and low quality reads.The filtered data were then mapped to the zebrafish reference genome danRer7 by STAR version: STAR 2.5.3a modified with following parameters: outSAMstrandField intronMotif outSAMattributes All outSAMunmapped Within outSAMattrIHstart 0 outWigStrand Stranded outFilterMultimapNmax 20 twopassMode Basic. All STAR ChIP seq reads were aligned to the zebrafish reference genome danRer7 using Bowtie2 version 2.2.2 Langmead and Salzberg 2012 with the parameters –t –q –N 1 –L 25. All unmapped reads non uniquely mapped reads and PCR duplicates were removed. For downstream analysis the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced RPKM. All STEM seq datasets were mapped to the danRer7 reference genome by Bismark Krueger and Andrews 2011. Reads were trimmed with cutadaptor Martin 2011 using parameters: minimum length 20 pair filter=any. Alignments were performed with the following parameters: N 1 X 600 score min L 0 0.6. Multi mapped reads and PCR duplicates were removed. bismark methylation extractor was used to calculate the DNA methylation level Genome build: danRer7 Supplementary files format and content: Bigwig for ChIP seq and RNA seq tracks gene expression table for RNA seq data	oocyte	The ovaries of adult female were isolated and transferred into specific buffer 5.4 mM KCl 136.8 mM NaCl 4.2 mM NaHCO3 0.44 mM KH2PO4 0.25 mM Na2HPO4 and 0.5% wt/vol BSA. Then stage I V oocytes were separated from the ovary with tweezers under microscope according to their morphology and the surrounding follicle cells were detached gently as much as possible.	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols 5 ug RNA was DNase I Fermentas Cat # EN0521 treated at 37C for 1 h. RNA was then purified using AMPure beads. Poly A tailed mRNA was collected using DynabeadsTM mRNA purification kit Invitrogen Cat # 61006. Purified RNA was fragmented with RNA Frag. Buffer NEB Cat # E6186A at 95C for 5 min. Reaction was stopped and RNA was purified by AMPure beads. First stand cDNA was synthesized with a commercial kit using both oligo dT and random primers Invitrogen Cat # 18080 051. Second strand cDNA was synthesized with second strand synthesis buffer Invitrogen Cat # 10812014 MgCl2 DTT dNTP dUTP RNase H Fermentas Cat # EN0202 E. coli DNA ligase NEB Cat # M0205S and DNA polymerase I NEB Cat # M0209S. DNA was purified post 2 hrs incubation on thermomixer at 16C. Synthesized cDNA was subjected to library preparation. DNA was end repaired adenylated and ligated to TruSeq sequencing adaptors. Libraries were then treated with UDG AMPErase Cat # N808 0096 at 37C for 1 hour followed by DNA amplification using Phusion HF DNA polymerase NEB Cat # M0530L. The amplified DNA was size selected using AMPure Beads for 200 500 bp DNA fragments.	The wild type Tu female strain were raised as standard protocol.	developmental stage:stage III\|cell type:prophase I oocyte\|strain:Tu	GSM3359499	GSM3359499: oocyte III RNA seq; Danio rerio; RNA Seq	GSM3359499		1	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols 5 ug RNA was DNase I Fermentas Cat # EN0521 treated at 37C for 1 h. RNA was then purified using AMPure beads. Poly A tailed mRNA was collected using DynabeadsTM mRNA purification kit Invitrogen Cat # 61006. Purified RNA was fragmented with RNA Frag. Buffer NEB Cat # E6186A at 95C for 5 min. Reaction was stopped and RNA was purified by AMPure beads. First stand cDNA was synthesized with a commercial kit using both oligo dT and random primers Invitrogen Cat # 18080 051. Second strand cDNA was synthesized with second strand synthesis buffer Invitrogen Cat # 10812014 MgCl2 DTT dNTP dUTP RNase H Fermentas Cat # EN0202 E. coli DNA ligase NEB Cat # M0205S and DNA polymerase I NEB Cat # M0209S. DNA was purified post 2 hrs incubation on thermomixer at 16C. Synthesized cDNA was subjected to library preparation. DNA was end repaired adenylated and ligated to TruSeq sequencing adaptors. Libraries were then treated with UDG AMPErase Cat # N808 0096 at 37C for 1 hour followed by DNA amplification using Phusion HF DNA polymerase NEB Cat # M0530L. The amplified DNA was size selected using AMPure Beads for 200 500 bp DNA fragments.	GEO Accession:GSM3359499	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 1500		SRP149356			oocyte_III_RNA_seq_r1.fq.gz	fastq	637289296.0	13005904.0	GSM3359499 r1	0:49 1:0	A:160396576;C:153811544;G:160426381;T:162544723;N:110072	49	0	160396576	153811544	160426381	162544723	110072	SRX4617973	SRS3720954	SRA712563	GEO	Tsinghua University	1	0.93382	0.03044	0.729	0.46965	49	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2018-08-28	Zygote	Embryo	Oocyte	Reproductive System
48339	48339	SRR7762355	SRX4617972	SRS3720944	SRP149356	PRJNA473799	Widespread enhancer dememorization and promoter priming during parental to zygotic transition	GSE114954	Other	The epigenome plays critical roles in controlling gene expression and development. However how the parental epigenomes transit to the zygotic epigenome in early development remains elusive. Here we show parental to zygotic transition in zebrafish involves extensive erasure of parental epigenetic memory starting by methylating gametic enhancers. Surprisingly this occurs even prior to fertilization for sperm. Both parental enhancers lose histone marks by the 4 cell stage and zygotic enhancers are not activated until around zygotic genome activation ZGA. By contrast many promoters remain hypomethylated and unexpectedly acquire de novo histone acetylation as early as at the 4 cell stage. They then resolve into either activated or repressed promoters upon ZGA. Maternal depletion of histone acetyltransferases results in aberrant ZGA and early embryonic lethality. Finally such reprogramming is largely driven by maternal factors with zygotic products contributing to embryonic enhancer activation. Thus these data revealed widespread enhancer dememorization and promoter priming during parental to zygotic transition. Overall design: By employing STAR ChIP seq and RNA seq we systematically examined the genome wide presence of H3K4me3 H3K27ac H3K27me3 and H3K36me3 in sperm oocyte 4 cell 256 cell and dome stage embryos.		pubmed:30444999		oocyte II RNA seq	GSM3359498		tissue:oocyte\|developmental stage:stage II\|cell type:S phase oocyte\|strain:Tu	oocyte II RNA seq	RNA seq data were firstly processed using Trim Galore! with default parameters to trim the adapter containing and low quality reads.The filtered data were then mapped to the zebrafish reference genome danRer7 by STAR version: STAR 2.5.3a modified with following parameters: outSAMstrandField intronMotif outSAMattributes All outSAMunmapped Within outSAMattrIHstart 0 outWigStrand Stranded outFilterMultimapNmax 20 twopassMode Basic. All STAR ChIP seq reads were aligned to the zebrafish reference genome danRer7 using Bowtie2 version 2.2.2 Langmead and Salzberg 2012 with the parameters –t –q –N 1 –L 25. All unmapped reads non uniquely mapped reads and PCR duplicates were removed. For downstream analysis the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced RPKM. All STEM seq datasets were mapped to the danRer7 reference genome by Bismark Krueger and Andrews 2011. Reads were trimmed with cutadaptor Martin 2011 using parameters: minimum length 20 pair filter=any. Alignments were performed with the following parameters: N 1 X 600 score min L 0 0.6. Multi mapped reads and PCR duplicates were removed. bismark methylation extractor was used to calculate the DNA methylation level Genome build: danRer7 Supplementary files format and content: Bigwig for ChIP seq and RNA seq tracks gene expression table for RNA seq data	oocyte	The ovaries of adult female were isolated and transferred into specific buffer 5.4 mM KCl 136.8 mM NaCl 4.2 mM NaHCO3 0.44 mM KH2PO4 0.25 mM Na2HPO4 and 0.5% wt/vol BSA. Then stage I V oocytes were separated from the ovary with tweezers under microscope according to their morphology and the surrounding follicle cells were detached gently as much as possible.	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols 5 ug RNA was DNase I Fermentas Cat # EN0521 treated at 37C for 1 h. RNA was then purified using AMPure beads. Poly A tailed mRNA was collected using DynabeadsTM mRNA purification kit Invitrogen Cat # 61006. Purified RNA was fragmented with RNA Frag. Buffer NEB Cat # E6186A at 95C for 5 min. Reaction was stopped and RNA was purified by AMPure beads. First stand cDNA was synthesized with a commercial kit using both oligo dT and random primers Invitrogen Cat # 18080 051. Second strand cDNA was synthesized with second strand synthesis buffer Invitrogen Cat # 10812014 MgCl2 DTT dNTP dUTP RNase H Fermentas Cat # EN0202 E. coli DNA ligase NEB Cat # M0205S and DNA polymerase I NEB Cat # M0209S. DNA was purified post 2 hrs incubation on thermomixer at 16C. Synthesized cDNA was subjected to library preparation. DNA was end repaired adenylated and ligated to TruSeq sequencing adaptors. Libraries were then treated with UDG AMPErase Cat # N808 0096 at 37C for 1 hour followed by DNA amplification using Phusion HF DNA polymerase NEB Cat # M0530L. The amplified DNA was size selected using AMPure Beads for 200 500 bp DNA fragments.	The wild type Tu female strain were raised as standard protocol.	developmental stage:stage II\|cell type:S phase oocyte\|strain:Tu	GSM3359498	GSM3359498: oocyte II RNA seq; Danio rerio; RNA Seq	GSM3359498		1	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols 5 ug RNA was DNase I Fermentas Cat # EN0521 treated at 37C for 1 h. RNA was then purified using AMPure beads. Poly A tailed mRNA was collected using DynabeadsTM mRNA purification kit Invitrogen Cat # 61006. Purified RNA was fragmented with RNA Frag. Buffer NEB Cat # E6186A at 95C for 5 min. Reaction was stopped and RNA was purified by AMPure beads. First stand cDNA was synthesized with a commercial kit using both oligo dT and random primers Invitrogen Cat # 18080 051. Second strand cDNA was synthesized with second strand synthesis buffer Invitrogen Cat # 10812014 MgCl2 DTT dNTP dUTP RNase H Fermentas Cat # EN0202 E. coli DNA ligase NEB Cat # M0205S and DNA polymerase I NEB Cat # M0209S. DNA was purified post 2 hrs incubation on thermomixer at 16C. Synthesized cDNA was subjected to library preparation. DNA was end repaired adenylated and ligated to TruSeq sequencing adaptors. Libraries were then treated with UDG AMPErase Cat # N808 0096 at 37C for 1 hour followed by DNA amplification using Phusion HF DNA polymerase NEB Cat # M0530L. The amplified DNA was size selected using AMPure Beads for 200 500 bp DNA fragments.	GEO Accession:GSM3359498	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 1500		SRP149356			oocyte_II_RNA_seq_r1.fq.gz	fastq	636518379.0	12990171.0	GSM3359498 r1	0:49 1:0	A:160017029;C:153897668;G:159821522;T:162670200;N:111960	49	0	160017029	153897668	159821522	162670200	111960	SRX4617972	SRS3720944	SRA712563	GEO	Tsinghua University	1	0.9326	0.0241	0.74073	0.47431	49	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2018-08-28	Zygote	Embryo	Oocyte	Reproductive System
48340	48340	SRR7762354	SRX4617971	SRS3720943	SRP149356	PRJNA473799	Widespread enhancer dememorization and promoter priming during parental to zygotic transition	GSE114954	Other	The epigenome plays critical roles in controlling gene expression and development. However how the parental epigenomes transit to the zygotic epigenome in early development remains elusive. Here we show parental to zygotic transition in zebrafish involves extensive erasure of parental epigenetic memory starting by methylating gametic enhancers. Surprisingly this occurs even prior to fertilization for sperm. Both parental enhancers lose histone marks by the 4 cell stage and zygotic enhancers are not activated until around zygotic genome activation ZGA. By contrast many promoters remain hypomethylated and unexpectedly acquire de novo histone acetylation as early as at the 4 cell stage. They then resolve into either activated or repressed promoters upon ZGA. Maternal depletion of histone acetyltransferases results in aberrant ZGA and early embryonic lethality. Finally such reprogramming is largely driven by maternal factors with zygotic products contributing to embryonic enhancer activation. Thus these data revealed widespread enhancer dememorization and promoter priming during parental to zygotic transition. Overall design: By employing STAR ChIP seq and RNA seq we systematically examined the genome wide presence of H3K4me3 H3K27ac H3K27me3 and H3K36me3 in sperm oocyte 4 cell 256 cell and dome stage embryos.		pubmed:30444999		oocyte I RNA seq	GSM3359497		tissue:oocyte\|developmental stage:stage I\|cell type:G1 phase oocyte\|strain:Tu	oocyte I RNA seq	RNA seq data were firstly processed using Trim Galore! with default parameters to trim the adapter containing and low quality reads.The filtered data were then mapped to the zebrafish reference genome danRer7 by STAR version: STAR 2.5.3a modified with following parameters: outSAMstrandField intronMotif outSAMattributes All outSAMunmapped Within outSAMattrIHstart 0 outWigStrand Stranded outFilterMultimapNmax 20 twopassMode Basic. All STAR ChIP seq reads were aligned to the zebrafish reference genome danRer7 using Bowtie2 version 2.2.2 Langmead and Salzberg 2012 with the parameters –t –q –N 1 –L 25. All unmapped reads non uniquely mapped reads and PCR duplicates were removed. For downstream analysis the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced RPKM. All STEM seq datasets were mapped to the danRer7 reference genome by Bismark Krueger and Andrews 2011. Reads were trimmed with cutadaptor Martin 2011 using parameters: minimum length 20 pair filter=any. Alignments were performed with the following parameters: N 1 X 600 score min L 0 0.6. Multi mapped reads and PCR duplicates were removed. bismark methylation extractor was used to calculate the DNA methylation level Genome build: danRer7 Supplementary files format and content: Bigwig for ChIP seq and RNA seq tracks gene expression table for RNA seq data	oocyte	The ovaries of adult female were isolated and transferred into specific buffer 5.4 mM KCl 136.8 mM NaCl 4.2 mM NaHCO3 0.44 mM KH2PO4 0.25 mM Na2HPO4 and 0.5% wt/vol BSA. Then stage I V oocytes were separated from the ovary with tweezers under microscope according to their morphology and the surrounding follicle cells were detached gently as much as possible.	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols 5 ug RNA was DNase I Fermentas Cat # EN0521 treated at 37C for 1 h. RNA was then purified using AMPure beads. Poly A tailed mRNA was collected using DynabeadsTM mRNA purification kit Invitrogen Cat # 61006. Purified RNA was fragmented with RNA Frag. Buffer NEB Cat # E6186A at 95C for 5 min. Reaction was stopped and RNA was purified by AMPure beads. First stand cDNA was synthesized with a commercial kit using both oligo dT and random primers Invitrogen Cat # 18080 051. Second strand cDNA was synthesized with second strand synthesis buffer Invitrogen Cat # 10812014 MgCl2 DTT dNTP dUTP RNase H Fermentas Cat # EN0202 E. coli DNA ligase NEB Cat # M0205S and DNA polymerase I NEB Cat # M0209S. DNA was purified post 2 hrs incubation on thermomixer at 16C. Synthesized cDNA was subjected to library preparation. DNA was end repaired adenylated and ligated to TruSeq sequencing adaptors. Libraries were then treated with UDG AMPErase Cat # N808 0096 at 37C for 1 hour followed by DNA amplification using Phusion HF DNA polymerase NEB Cat # M0530L. The amplified DNA was size selected using AMPure Beads for 200 500 bp DNA fragments.	The wild type Tu female strain were raised as standard protocol.	developmental stage:stage I\|cell type:G1 phase oocyte\|strain:Tu	GSM3359497	GSM3359497: oocyte I RNA seq; Danio rerio; RNA Seq	GSM3359497		1	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols 5 ug RNA was DNase I Fermentas Cat # EN0521 treated at 37C for 1 h. RNA was then purified using AMPure beads. Poly A tailed mRNA was collected using DynabeadsTM mRNA purification kit Invitrogen Cat # 61006. Purified RNA was fragmented with RNA Frag. Buffer NEB Cat # E6186A at 95C for 5 min. Reaction was stopped and RNA was purified by AMPure beads. First stand cDNA was synthesized with a commercial kit using both oligo dT and random primers Invitrogen Cat # 18080 051. Second strand cDNA was synthesized with second strand synthesis buffer Invitrogen Cat # 10812014 MgCl2 DTT dNTP dUTP RNase H Fermentas Cat # EN0202 E. coli DNA ligase NEB Cat # M0205S and DNA polymerase I NEB Cat # M0209S. DNA was purified post 2 hrs incubation on thermomixer at 16C. Synthesized cDNA was subjected to library preparation. DNA was end repaired adenylated and ligated to TruSeq sequencing adaptors. Libraries were then treated with UDG AMPErase Cat # N808 0096 at 37C for 1 hour followed by DNA amplification using Phusion HF DNA polymerase NEB Cat # M0530L. The amplified DNA was size selected using AMPure Beads for 200 500 bp DNA fragments.	GEO Accession:GSM3359497	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 1500		SRP149356			oocyte_I_RNA_seq_r1.fq.gz	fastq	637062181.0	13001269.0	GSM3359497 r1	0:49 1:0	A:161520633;C:153547778;G:156542304;T:165341706;N:109760	49	0	161520633	153547778	156542304	165341706	109760	SRX4617971	SRS3720943	SRA712563	GEO	Tsinghua University	1	0.92933	0.02356	0.73683	0.47367	49	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2018-08-28	Zygote	Embryo	Oocyte	Reproductive System
48812	48812	SRR7341816	SRX4215318	SRS3417596	SRP150521	PRJNA476105	Transcriptome analysis of wildtype and sox3 / zebrafish adult ovary	GSE115806	Transcriptome Analysis	The goals of this study are to compare the differentially expressed genes between wildtype and sox3 / zebrafish ovaries based on RNA seq data and some of these genes were validated by qRT–PCR. Further the differentially expressed genes were devided into up regulated and down regulated genes for GO and KEGG analysis. Overall design: Ovary mRNA profiles of adult wildtype and sox3 / zebrafish were generated by deep sequencing.		pubmed:30588557		KO mix	GSM3190267		source name:Ovary\|strain:AB\|tissue:Ovary\|age:Adult	KO mix	Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz10 whole genome using HISAT mapped to genes using Bowtie2. fragments per kilo bases per million fragments FPKM were calculated using RSEM. Genome build: GRCz10 Supplementary files format and content: The text files include the Ensembl ID of genes and the FPKM values for each Sample.	Ovary		Ovaries were isolated frozen on dry ice and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols.		strain:AB\|tissue:Ovary\|age:Adult	GSM3190267	GSM3190267: KO mix; Danio rerio; RNA Seq	GSM3190267		1	Ovaries were isolated frozen on dry ice and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols.	GEO Accession:GSM3190267	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500		SRP150521			KO-ovary.fq.gz	fastq	1173123100.0	23462462.0	GSM3190267 r1	0:50 1:0	A:308426188;C:271468505;G:292019086;T:300532126;N:677195	50	0	308426188	271468505	292019086	300532126	677195	SRX4215318	SRS3417596	SRA721702	GEO	Wuhan university	1	0.93261	0.02261	0.76132	0.4585	50	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2018-06-14	Adult	Adult	Gonad	Reproductive System
48813	48813	SRR7341815	SRX4215317	SRS3417595	SRP150521	PRJNA476105	Transcriptome analysis of wildtype and sox3 / zebrafish adult ovary	GSE115806	Transcriptome Analysis	The goals of this study are to compare the differentially expressed genes between wildtype and sox3 / zebrafish ovaries based on RNA seq data and some of these genes were validated by qRT–PCR. Further the differentially expressed genes were devided into up regulated and down regulated genes for GO and KEGG analysis. Overall design: Ovary mRNA profiles of adult wildtype and sox3 / zebrafish were generated by deep sequencing.		pubmed:30588557		WT mix	GSM3190266		source name:Ovary\|strain:AB\|tissue:Ovary\|age:Adult	WT mix	Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz10 whole genome using HISAT mapped to genes using Bowtie2. fragments per kilo bases per million fragments FPKM were calculated using RSEM. Genome build: GRCz10 Supplementary files format and content: The text files include the Ensembl ID of genes and the FPKM values for each Sample.	Ovary		Ovaries were isolated frozen on dry ice and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols.		strain:AB\|tissue:Ovary\|age:Adult	GSM3190266	GSM3190266: WT mix; Danio rerio; RNA Seq	GSM3190266		1	Ovaries were isolated frozen on dry ice and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols.	GEO Accession:GSM3190266	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	BGISEQ	BGISEQ-500		SRP150521			WT-ovary.fq.gz	fastq	1176463600.0	23529272.0	GSM3190266 r1	0:50 1:0	A:311869864;C:270650722;G:289863261;T:303489229;N:590524	50	0	311869864	270650722	289863261	303489229	590524	SRX4215317	SRS3417595	SRA721702	GEO	Wuhan university	1	0.93489	0.02765	0.75627	0.46875	50	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2018-06-14	Adult	Adult	Gonad	Reproductive System
48911	48911	SRR7468702	SRX4338471	SRS3499386	SRP151935	PRJNA479503	Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens	GSE116611	Transcriptome Analysis	post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples		pubmed:31597660;pubmed:33589679		Testis Recovery 5	GSM3243777		source name:Testis\|age:Adult\|genotype:Wild type\|tissue:Testis	Testis Recovery 5	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|tissue:Testis	GSM3243777	GSM3243777: Testis Recovery 5; Danio rerio; RNA Seq	GSM3243777		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer's protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer's instructions	GEO Accession:GSM3243777	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP151935			ZFG-14-10_27_ACTTGA_L001_R1_001_HBGRYADXX.fastq.gz	fastq	552604890.0	10835390.0	GSM3243777 r1	0:51	A:139121742;C:132482814;G:122480393;T:158489534;N:30407	51		139121742	132482814	122480393	158489534	30407	SRX4338471	SRS3499386	SRA732862	GEO	Reproductive Biology, Biology, Utrecht University	1	0.92201	0.11734	0.63711	0.47964	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2018-07-03	Adult	Adult	Gonad	Reproductive System
48912	48912	SRR7468703	SRX4338471	SRS3499386	SRP151935	PRJNA479503	Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens	GSE116611	Transcriptome Analysis	post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples		pubmed:31597660;pubmed:33589679		Testis Recovery 5	GSM3243777		source name:Testis\|age:Adult\|genotype:Wild type\|tissue:Testis	Testis Recovery 5	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|tissue:Testis	GSM3243777	GSM3243777: Testis Recovery 5; Danio rerio; RNA Seq	GSM3243777		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer's protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer's instructions	GEO Accession:GSM3243777	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP151935			ZFG-14-10_27_ACTTGA_L002_R1_001_HBGRYADXX.fastq.gz	fastq	545267673.0	10691523.0	GSM3243777 r2	0:51	A:137207619;C:130755783;G:120931785;T:156332365;N:40121	51		137207619	130755783	120931785	156332365	40121	SRX4338471	SRS3499386	SRA732862	GEO	Reproductive Biology, Biology, Utrecht University	1	0.92138	0.11738	0.64098	0.48487	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2018-07-03	Adult	Adult	Gonad	Reproductive System
48913	48913	SRR7468700	SRX4338470	SRS3499384	SRP151935	PRJNA479503	Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens	GSE116611	Transcriptome Analysis	post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples		pubmed:31597660;pubmed:33589679		Testis Recovery 4	GSM3243776		source name:Testis\|age:Adult\|genotype:Wild type\|tissue:Testis	Testis Recovery 4	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|tissue:Testis	GSM3243776	GSM3243776: Testis Recovery 4; Danio rerio; RNA Seq	GSM3243776		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer's protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer's instructions	GEO Accession:GSM3243776	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP151935			ZFG-14-10_22_TTAGGC_L001_R1_001_HBGRYADXX.fastq.gz	fastq	350250966.0	6867666.0	GSM3243776 r1	0:51	A:90857323;C:81141631;G:77474341;T:100758696;N:18975	51		90857323	81141631	77474341	100758696	18975	SRX4338470	SRS3499384	SRA732862	GEO	Reproductive Biology, Biology, Utrecht University	1	0.92353	0.11575	0.64788	0.49422	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2018-07-03	Adult	Adult	Gonad	Reproductive System
48914	48914	SRR7468701	SRX4338470	SRS3499384	SRP151935	PRJNA479503	Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens	GSE116611	Transcriptome Analysis	post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples		pubmed:31597660;pubmed:33589679		Testis Recovery 4	GSM3243776		source name:Testis\|age:Adult\|genotype:Wild type\|tissue:Testis	Testis Recovery 4	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|tissue:Testis	GSM3243776	GSM3243776: Testis Recovery 4; Danio rerio; RNA Seq	GSM3243776		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer's protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer's instructions	GEO Accession:GSM3243776	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP151935			ZFG-14-10_22_TTAGGC_L002_R1_001_HBGRYADXX.fastq.gz	fastq	345190491.0	6768441.0	GSM3243776 r2	0:51	A:89503841;C:79992303;G:76416649;T:99253801;N:23897	51		89503841	79992303	76416649	99253801	23897	SRX4338470	SRS3499384	SRA732862	GEO	Reproductive Biology, Biology, Utrecht University	1	0.92144	0.11503	0.64715	0.4912	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2018-07-03	Adult	Adult	Gonad	Reproductive System
48915	48915	SRR7468698	SRX4338469	SRS3499387	SRP151935	PRJNA479503	Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens	GSE116611	Transcriptome Analysis	post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples		pubmed:31597660;pubmed:33589679		Testis Recovery 3	GSM3243775		source name:Testis\|age:Adult\|genotype:Wild type\|tissue:Testis	Testis Recovery 3	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|tissue:Testis	GSM3243775	GSM3243775: Testis Recovery 3; Danio rerio; RNA Seq	GSM3243775		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer's protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer's instructions	GEO Accession:GSM3243775	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP151935			ZFG-14-10_21_ATCACG_L001_R1_001_HBGRYADXX.fastq.gz	fastq	932153673.0	18277523.0	GSM3243775 r1	0:51	A:233867020;C:223302964;G:204457194;T:270472757;N:53738	51		233867020	223302964	204457194	270472757	53738	SRX4338469	SRS3499387	SRA732862	GEO	Reproductive Biology, Biology, Utrecht University	1	0.9252	0.10721	0.6477	0.48926	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2018-07-03	Adult	Adult	Gonad	Reproductive System
48916	48916	SRR7468699	SRX4338469	SRS3499387	SRP151935	PRJNA479503	Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens	GSE116611	Transcriptome Analysis	post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples		pubmed:31597660;pubmed:33589679		Testis Recovery 3	GSM3243775		source name:Testis\|age:Adult\|genotype:Wild type\|tissue:Testis	Testis Recovery 3	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|tissue:Testis	GSM3243775	GSM3243775: Testis Recovery 3; Danio rerio; RNA Seq	GSM3243775		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer's protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer's instructions	GEO Accession:GSM3243775	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP151935			ZFG-14-10_21_ATCACG_L002_R1_001_HBGRYADXX.fastq.gz	fastq	923872752.0	18115152.0	GSM3243775 r2	0:51	A:231644800;C:221350765;G:202799132;T:268008161;N:69894	51		231644800	221350765	202799132	268008161	69894	SRX4338469	SRS3499387	SRA732862	GEO	Reproductive Biology, Biology, Utrecht University	1	0.92438	0.1075	0.64749	0.49122	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2018-07-03	Adult	Adult	Gonad	Reproductive System
48917	48917	SRR7468696	SRX4338468	SRS3499385	SRP151935	PRJNA479503	Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens	GSE116611	Transcriptome Analysis	post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples		pubmed:31597660;pubmed:33589679		Testis Recovery 2	GSM3243774		source name:Testis\|age:Adult\|genotype:Wild type\|tissue:Testis	Testis Recovery 2	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|tissue:Testis	GSM3243774	GSM3243774: Testis Recovery 2; Danio rerio; RNA Seq	GSM3243774		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer's protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer's instructions	GEO Accession:GSM3243774	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP151935			ZFG-14-10_20_GTGAAA_L001_R1_001_HBGRYADXX.fastq.gz	fastq	488463975.0	9577725.0	GSM3243774 r1	0:51	A:124059246;C:115925214;G:108132371;T:140316066;N:31078	51		124059246	115925214	108132371	140316066	31078	SRX4338468	SRS3499385	SRA732862	GEO	Reproductive Biology, Biology, Utrecht University	1	0.92666	0.10881	0.6406	0.48975	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2018-07-03	Adult	Adult	Gonad	Reproductive System
48918	48918	SRR7468697	SRX4338468	SRS3499385	SRP151935	PRJNA479503	Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens	GSE116611	Transcriptome Analysis	post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples		pubmed:31597660;pubmed:33589679		Testis Recovery 2	GSM3243774		source name:Testis\|age:Adult\|genotype:Wild type\|tissue:Testis	Testis Recovery 2	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|tissue:Testis	GSM3243774	GSM3243774: Testis Recovery 2; Danio rerio; RNA Seq	GSM3243774		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer's protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer's instructions	GEO Accession:GSM3243774	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP151935			ZFG-14-10_20_GTGAAA_L002_R1_001_HBGRYADXX.fastq.gz	fastq	483820986.0	9486686.0	GSM3243774 r2	0:51	A:122808323;C:114849749;G:107201486;T:138922696;N:38732	51		122808323	114849749	107201486	138922696	38732	SRX4338468	SRS3499385	SRA732862	GEO	Reproductive Biology, Biology, Utrecht University	1	0.92627	0.10747	0.6369	0.49158	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2018-07-03	Adult	Adult	Gonad	Reproductive System
48919	48919	SRR7468694	SRX4338467	SRS3499381	SRP151935	PRJNA479503	Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens	GSE116611	Transcriptome Analysis	post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples		pubmed:31597660;pubmed:33589679		Testis Recovery 1	GSM3243773		source name:Testis\|age:Adult\|genotype:Wild type\|tissue:Testis	Testis Recovery 1	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|tissue:Testis	GSM3243773	GSM3243773: Testis Recovery 1; Danio rerio; RNA Seq	GSM3243773		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer's protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer's instructions	GEO Accession:GSM3243773	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP151935			ZFG-14-10_19_GTCCGC_L001_R1_001_HBGRYADXX.fastq.gz	fastq	320008476.0	6274676.0	GSM3243773 r1	0:51	A:82056407;C:75200770;G:70054966;T:92678428;N:17905	51		82056407	75200770	70054966	92678428	17905	SRX4338467	SRS3499381	SRA732862	GEO	Reproductive Biology, Biology, Utrecht University	1	0.92363	0.11205	0.63901	0.49533	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2018-07-03	Adult	Adult	Gonad	Reproductive System
48920	48920	SRR7468695	SRX4338467	SRS3499381	SRP151935	PRJNA479503	Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens	GSE116611	Transcriptome Analysis	post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples		pubmed:31597660;pubmed:33589679		Testis Recovery 1	GSM3243773		source name:Testis\|age:Adult\|genotype:Wild type\|tissue:Testis	Testis Recovery 1	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|tissue:Testis	GSM3243773	GSM3243773: Testis Recovery 1; Danio rerio; RNA Seq	GSM3243773		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer's protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer's instructions	GEO Accession:GSM3243773	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP151935			ZFG-14-10_19_GTCCGC_L002_R1_001_HBGRYADXX.fastq.gz	fastq	316706379.0	6209929.0	GSM3243773 r2	0:51	A:81144248;C:74436278;G:69378013;T:91724817;N:23023	51		81144248	74436278	69378013	91724817	23023	SRX4338467	SRS3499381	SRA732862	GEO	Reproductive Biology, Biology, Utrecht University	1	0.92209	0.11247	0.641	0.49169	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2018-07-03	Adult	Adult	Gonad	Reproductive System
48921	48921	SRR7468692	SRX4338466	SRS3499380	SRP151935	PRJNA479503	Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens	GSE116611	Transcriptome Analysis	post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples		pubmed:31597660;pubmed:33589679		Testis Depletion 5	GSM3243772		source name:Testis\|age:Adult\|genotype:Wild type\|tissue:Testis	Testis Depletion 5	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|tissue:Testis	GSM3243772	GSM3243772: Testis Depletion 5; Danio rerio; RNA Seq	GSM3243772		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer's protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer's instructions	GEO Accession:GSM3243772	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP151935			ZFG-14-10_15_CCGTCC_L001_R1_001_HBGRYADXX.fastq.gz	fastq	361757892.0	7093292.0	GSM3243772 r1	0:51	A:91765393;C:86319849;G:81580662;T:102070154;N:21834	51		91765393	86319849	81580662	102070154	21834	SRX4338466	SRS3499380	SRA732862	GEO	Reproductive Biology, Biology, Utrecht University	1	0.91403	0.09146	0.70303	0.47815	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2018-07-03	Adult	Adult	Gonad	Reproductive System
48922	48922	SRR7468693	SRX4338466	SRS3499380	SRP151935	PRJNA479503	Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens	GSE116611	Transcriptome Analysis	post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples		pubmed:31597660;pubmed:33589679		Testis Depletion 5	GSM3243772		source name:Testis\|age:Adult\|genotype:Wild type\|tissue:Testis	Testis Depletion 5	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|tissue:Testis	GSM3243772	GSM3243772: Testis Depletion 5; Danio rerio; RNA Seq	GSM3243772		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer's protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer's instructions	GEO Accession:GSM3243772	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP151935			ZFG-14-10_15_CCGTCC_L002_R1_001_HBGRYADXX.fastq.gz	fastq	358933155.0	7037905.0	GSM3243772 r2	0:51	A:90971855;C:85661708;G:81025594;T:101247515;N:26483	51		90971855	85661708	81025594	101247515	26483	SRX4338466	SRS3499380	SRA732862	GEO	Reproductive Biology, Biology, Utrecht University	1	0.91352	0.09218	0.70587	0.47689	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2018-07-03	Adult	Adult	Gonad	Reproductive System
48923	48923	SRR7468690	SRX4338465	SRS3499373	SRP151935	PRJNA479503	Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens	GSE116611	Transcriptome Analysis	post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples		pubmed:31597660;pubmed:33589679		Testis Depletion 4	GSM3243771		source name:Testis\|age:Adult\|genotype:Wild type\|tissue:Testis	Testis Depletion 4	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|tissue:Testis	GSM3243771	GSM3243771: Testis Depletion 4; Danio rerio; RNA Seq	GSM3243771		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer's protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer's instructions	GEO Accession:GSM3243771	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP151935			ZFG-14-10_13_ATGTCA_L001_R1_001_HBGRYADXX.fastq.gz	fastq	362189301.0	7101751.0	GSM3243771 r1	0:51	A:93944703;C:84574406;G:80766474;T:102881135;N:22583	51		93944703	84574406	80766474	102881135	22583	SRX4338465	SRS3499373	SRA732862	GEO	Reproductive Biology, Biology, Utrecht University	1	0.9175	0.13669	0.69331	0.47497	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2018-07-03	Adult	Adult	Gonad	Reproductive System
48924	48924	SRR7468691	SRX4338465	SRS3499373	SRP151935	PRJNA479503	Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens	GSE116611	Transcriptome Analysis	post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples		pubmed:31597660;pubmed:33589679		Testis Depletion 4	GSM3243771		source name:Testis\|age:Adult\|genotype:Wild type\|tissue:Testis	Testis Depletion 4	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|tissue:Testis	GSM3243771	GSM3243771: Testis Depletion 4; Danio rerio; RNA Seq	GSM3243771		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer's protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer's instructions	GEO Accession:GSM3243771	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP151935			ZFG-14-10_13_ATGTCA_L002_R1_001_HBGRYADXX.fastq.gz	fastq	357458796.0	7008996.0	GSM3243771 r2	0:51	A:92666882;C:83501967;G:79751404;T:101511030;N:27513	51		92666882	83501967	79751404	101511030	27513	SRX4338465	SRS3499373	SRA732862	GEO	Reproductive Biology, Biology, Utrecht University	1	0.91688	0.13791	0.69589	0.48069	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2018-07-03	Adult	Adult	Gonad	Reproductive System
48925	48925	SRR7468688	SRX4338464	SRS3499374	SRP151935	PRJNA479503	Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens	GSE116611	Transcriptome Analysis	post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples		pubmed:31597660;pubmed:33589679		Testis Depletion 3	GSM3243770		source name:Testis\|age:Adult\|genotype:Wild type\|tissue:Testis	Testis Depletion 3	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|tissue:Testis	GSM3243770	GSM3243770: Testis Depletion 3; Danio rerio; RNA Seq	GSM3243770		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer's protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer's instructions	GEO Accession:GSM3243770	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP151935			ZFG-14-10_12_AGTTCC_L001_R1_001_HBGRYADXX.fastq.gz	fastq	360587850.0	7070350.0	GSM3243770 r1	0:51	A:93351341;C:83525699;G:80405894;T:103285803;N:19113	51		93351341	83525699	80405894	103285803	19113	SRX4338464	SRS3499374	SRA732862	GEO	Reproductive Biology, Biology, Utrecht University	1	0.91686	0.15015	0.68749	0.48342	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2018-07-03	Adult	Adult	Gonad	Reproductive System
48926	48926	SRR7468689	SRX4338464	SRS3499374	SRP151935	PRJNA479503	Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens	GSE116611	Transcriptome Analysis	post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples		pubmed:31597660;pubmed:33589679		Testis Depletion 3	GSM3243770		source name:Testis\|age:Adult\|genotype:Wild type\|tissue:Testis	Testis Depletion 3	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|tissue:Testis	GSM3243770	GSM3243770: Testis Depletion 3; Danio rerio; RNA Seq	GSM3243770		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer's protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer's instructions	GEO Accession:GSM3243770	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP151935			ZFG-14-10_12_AGTTCC_L002_R1_001_HBGRYADXX.fastq.gz	fastq	355171395.0	6964145.0	GSM3243770 r2	0:51	A:91888828;C:82308089;G:79253121;T:101695969;N:25388	51		91888828	82308089	79253121	101695969	25388	SRX4338464	SRS3499374	SRA732862	GEO	Reproductive Biology, Biology, Utrecht University	1	0.91616	0.14982	0.68745	0.4751	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2018-07-03	Adult	Adult	Gonad	Reproductive System
48927	48927	SRR7468686	SRX4338463	SRS3499378	SRP151935	PRJNA479503	Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens	GSE116611	Transcriptome Analysis	post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples		pubmed:31597660;pubmed:33589679		Testis Depletion 2	GSM3243769		source name:Testis\|age:Adult\|genotype:Wild type\|tissue:Testis	Testis Depletion 2	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|tissue:Testis	GSM3243769	GSM3243769: Testis Depletion 2; Danio rerio; RNA Seq	GSM3243769		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer's protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer's instructions	GEO Accession:GSM3243769	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP151935			ZFG-14-10_11_AGTCAA_L001_R1_001_HBGRYADXX.fastq.gz	fastq	292081947.0	5727097.0	GSM3243769 r1	0:51	A:72873171;C:69857310;G:66617588;T:82718171;N:15707	51		72873171	69857310	66617588	82718171	15707	SRX4338463	SRS3499378	SRA732862	GEO	Reproductive Biology, Biology, Utrecht University	1	0.93	0.08674	0.65819	0.50939	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2018-07-03	Adult	Adult	Gonad	Reproductive System
48928	48928	SRR7468687	SRX4338463	SRS3499378	SRP151935	PRJNA479503	Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens	GSE116611	Transcriptome Analysis	post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples		pubmed:31597660;pubmed:33589679		Testis Depletion 2	GSM3243769		source name:Testis\|age:Adult\|genotype:Wild type\|tissue:Testis	Testis Depletion 2	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|tissue:Testis	GSM3243769	GSM3243769: Testis Depletion 2; Danio rerio; RNA Seq	GSM3243769		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer's protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer's instructions	GEO Accession:GSM3243769	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP151935			ZFG-14-10_11_AGTCAA_L002_R1_001_HBGRYADXX.fastq.gz	fastq	287484450.0	5636950.0	GSM3243769 r2	0:51	A:71715008;C:68762533;G:65604930;T:81381185;N:20794	51		71715008	68762533	65604930	81381185	20794	SRX4338463	SRS3499378	SRA732862	GEO	Reproductive Biology, Biology, Utrecht University	1	0.92956	0.0864	0.6589	0.49904	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2018-07-03	Adult	Adult	Gonad	Reproductive System
48929	48929	SRR7468684	SRX4338462	SRS3499376	SRP151935	PRJNA479503	Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens	GSE116611	Transcriptome Analysis	post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples		pubmed:31597660;pubmed:33589679		Testis Depletion 1	GSM3243768		source name:Testis\|age:Adult\|genotype:Wild type\|tissue:Testis	Testis Depletion 1	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|tissue:Testis	GSM3243768	GSM3243768: Testis Depletion 1; Danio rerio; RNA Seq	GSM3243768		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer's protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer's instructions	GEO Accession:GSM3243768	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP151935			ZFG-14-10_10_CTTGTA_L001_R1_001_HBGRYADXX.fastq.gz	fastq	321374715.0	6301465.0	GSM3243768 r1	0:51	A:82362320;C:75071563;G:70755128;T:93167038;N:18666	51		82362320	75071563	70755128	93167038	18666	SRX4338462	SRS3499376	SRA732862	GEO	Reproductive Biology, Biology, Utrecht University	1	0.9178	0.15168	0.64386	0.47826	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2018-07-03	Adult	Adult	Gonad	Reproductive System
48930	48930	SRR7468685	SRX4338462	SRS3499376	SRP151935	PRJNA479503	Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens	GSE116611	Transcriptome Analysis	post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples		pubmed:31597660;pubmed:33589679		Testis Depletion 1	GSM3243768		source name:Testis\|age:Adult\|genotype:Wild type\|tissue:Testis	Testis Depletion 1	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|tissue:Testis	GSM3243768	GSM3243768: Testis Depletion 1; Danio rerio; RNA Seq	GSM3243768		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer's protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer's instructions	GEO Accession:GSM3243768	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP151935			ZFG-14-10_10_CTTGTA_L002_R1_001_HBGRYADXX.fastq.gz	fastq	317659365.0	6228615.0	GSM3243768 r2	0:51	A:81382955;C:74232035;G:69983462;T:92037129;N:23784	51		81382955	74232035	69983462	92037129	23784	SRX4338462	SRS3499376	SRA732862	GEO	Reproductive Biology, Biology, Utrecht University	1	0.91676	0.15228	0.64425	0.4778	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2018-07-03	Adult	Adult	Gonad	Reproductive System
48931	48931	SRR7468682	SRX4338461	SRS3499379	SRP151935	PRJNA479503	Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens	GSE116611	Transcriptome Analysis	post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples		pubmed:31597660;pubmed:33589679		Testis Control 5	GSM3243767		source name:Testis\|age:Adult\|genotype:Wild type\|tissue:Testis	Testis Control 5	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|tissue:Testis	GSM3243767	GSM3243767: Testis Control 5; Danio rerio; RNA Seq	GSM3243767		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer's protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer's instructions	GEO Accession:GSM3243767	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP151935			ZFG-14-10_5_CAGATC_L001_R1_001_HBGRYADXX.fastq.gz	fastq	1807367325.0	35438575.0	GSM3243767 r1	0:51	A:452670863;C:426888853;G:402222075;T:525465400;N:120134	51		452670863	426888853	402222075	525465400	120134	SRX4338461	SRS3499379	SRA732862	GEO	Reproductive Biology, Biology, Utrecht University	1	0.92398	0.10727	0.63847	0.48929	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2018-07-03	Adult	Adult	Gonad	Reproductive System
48932	48932	SRR7468683	SRX4338461	SRS3499379	SRP151935	PRJNA479503	Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens	GSE116611	Transcriptome Analysis	post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples		pubmed:31597660;pubmed:33589679		Testis Control 5	GSM3243767		source name:Testis\|age:Adult\|genotype:Wild type\|tissue:Testis	Testis Control 5	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|tissue:Testis	GSM3243767	GSM3243767: Testis Control 5; Danio rerio; RNA Seq	GSM3243767		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer's protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer's instructions	GEO Accession:GSM3243767	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP151935			ZFG-14-10_5_CAGATC_L002_R1_001_HBGRYADXX.fastq.gz	fastq	1788601008.0	35070608.0	GSM3243767 r2	0:51	A:447675880;C:422557474;G:398397059;T:519829628;N:140967	51		447675880	422557474	398397059	519829628	140967	SRX4338461	SRS3499379	SRA732862	GEO	Reproductive Biology, Biology, Utrecht University	1	0.92324	0.10891	0.63954	0.4884	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2018-07-03	Adult	Adult	Gonad	Reproductive System
48933	48933	SRR7468680	SRX4338460	SRS3499377	SRP151935	PRJNA479503	Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens	GSE116611	Transcriptome Analysis	post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples		pubmed:31597660;pubmed:33589679		Testis Control 4	GSM3243766		source name:Testis\|age:Adult\|genotype:Wild type\|tissue:Testis	Testis Control 4	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|tissue:Testis	GSM3243766	GSM3243766: Testis Control 4; Danio rerio; RNA Seq	GSM3243766		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer's protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer's instructions	GEO Accession:GSM3243766	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP151935			ZFG-14-10_4_GCCAAT_L001_R1_001_HBGRYADXX.fastq.gz	fastq	432263454.0	8475754.0	GSM3243766 r1	0:51	A:108617721;C:101534969;G:96731457;T:125354102;N:25205	51		108617721	101534969	96731457	125354102	25205	SRX4338460	SRS3499377	SRA732862	GEO	Reproductive Biology, Biology, Utrecht University	1	0.92566	0.11169	0.64062	0.48877	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2018-07-03	Adult	Adult	Gonad	Reproductive System
48934	48934	SRR7468681	SRX4338460	SRS3499377	SRP151935	PRJNA479503	Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens	GSE116611	Transcriptome Analysis	post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples		pubmed:31597660;pubmed:33589679		Testis Control 4	GSM3243766		source name:Testis\|age:Adult\|genotype:Wild type\|tissue:Testis	Testis Control 4	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|tissue:Testis	GSM3243766	GSM3243766: Testis Control 4; Danio rerio; RNA Seq	GSM3243766		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer's protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer's instructions	GEO Accession:GSM3243766	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP151935			ZFG-14-10_4_GCCAAT_L002_R1_001_HBGRYADXX.fastq.gz	fastq	427837980.0	8388980.0	GSM3243766 r2	0:51	A:107459455;C:100505057;G:95801183;T:124040216;N:32069	51		107459455	100505057	95801183	124040216	32069	SRX4338460	SRS3499377	SRA732862	GEO	Reproductive Biology, Biology, Utrecht University	1	0.92497	0.11054	0.6422	0.49028	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2018-07-03	Adult	Adult	Gonad	Reproductive System
48935	48935	SRR7468678	SRX4338459	SRS3499375	SRP151935	PRJNA479503	Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens	GSE116611	Transcriptome Analysis	post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples		pubmed:31597660;pubmed:33589679		Testis Control 3	GSM3243765		source name:Testis\|age:Adult\|genotype:Wild type\|tissue:Testis	Testis Control 3	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|tissue:Testis	GSM3243765	GSM3243765: Testis Control 3; Danio rerio; RNA Seq	GSM3243765		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer's protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer's instructions	GEO Accession:GSM3243765	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP151935			ZFG-14-10_3_ACAGTG_L001_R1_001_HBGRYADXX.fastq.gz	fastq	318864342.0	6252242.0	GSM3243765 r1	0:51	A:79540177;C:75401356;G:70862416;T:93041977;N:18416	51		79540177	75401356	70862416	93041977	18416	SRX4338459	SRS3499375	SRA732862	GEO	Reproductive Biology, Biology, Utrecht University	1	0.92501	0.10543	0.64421	0.49318	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2018-07-03	Adult	Adult	Gonad	Reproductive System
48936	48936	SRR7468679	SRX4338459	SRS3499375	SRP151935	PRJNA479503	Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens	GSE116611	Transcriptome Analysis	post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples		pubmed:31597660;pubmed:33589679		Testis Control 3	GSM3243765		source name:Testis\|age:Adult\|genotype:Wild type\|tissue:Testis	Testis Control 3	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|tissue:Testis	GSM3243765	GSM3243765: Testis Control 3; Danio rerio; RNA Seq	GSM3243765		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer's protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer's instructions	GEO Accession:GSM3243765	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP151935			ZFG-14-10_3_ACAGTG_L002_R1_001_HBGRYADXX.fastq.gz	fastq	315012924.0	6176724.0	GSM3243765 r2	0:51	A:78549739;C:74486878;G:70065256;T:91887178;N:23873	51		78549739	74486878	70065256	91887178	23873	SRX4338459	SRS3499375	SRA732862	GEO	Reproductive Biology, Biology, Utrecht University	1	0.92419	0.10379	0.64648	0.4907	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2018-07-03	Adult	Adult	Gonad	Reproductive System
48937	48937	SRR7468676	SRX4338458	SRS3499372	SRP151935	PRJNA479503	Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens	GSE116611	Transcriptome Analysis	post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples		pubmed:31597660;pubmed:33589679		Testis Control 2	GSM3243764		source name:Testis\|age:Adult\|genotype:Wild type\|tissue:Testis	Testis Control 2	Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample	Testis		Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions		age:Adult\|genotype:Wild type\|tissue:Testis	GSM3243764	GSM3243764: Testis Control 2; Danio rerio; RNA Seq	GSM3243764		1	Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer's protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer's instructions	GEO Accession:GSM3243764	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP151935			ZFG-14-10_2_TGACCA_L001_R1_001_HBGRYADXX.fastq.gz	fastq	281993331.0	5529281.0	GSM3243764 r1	0:51	A:74248995;C:65166680;G:61565290;T:80996003;N:16363	51		74248995	65166680	61565290	80996003	16363	SRX4338458	SRS3499372	SRA732862	GEO	Reproductive Biology, Biology, Utrecht University	1	0.90812	0.08809	0.66565	0.48223	51	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Netherlands	2018-07-03	Adult	Adult	Gonad	Reproductive System

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