metadata: run_metadata: 52 rows where devstage_curation = "Zygote" and tissue

52 rows where devstage_curation = "Zygote" and tissue_curation = "Whole Organism"

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.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
30772	30772	SRR28348938	SRX23954958	SRS20755379	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 Embryo 0hpf rep3	GSM8147855	source name:Whole embryo\|tissue:Whole embryo\|developmental stage:0hpf\|genotype:AB TF and TLF\|geo loc name:missing\|collection date:missing	Zebrafish Embryo 0hpf rep3	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	Whole embryo		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:Whole embryo\|developmental stage:0hpf\|genotype:AB TF and TLF	GSM8147855	GSM8147855: Zebrafish Embryo 0hpf rep3; Danio rerio; RNA Seq	GSM8147855 r1	GSM8147855	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		s_0hpf_3.fastq	fastq	1542142220.0	20291345.0	GSM8147855 r1	0:76	A:376857497;C:381518368;G:357117823;T:426581588;N:66944	76		376857497	381518368	357117823	426581588	66944	SRX23954958	SRS20755379	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	Zygote	Embryo	Whole Organism	All anatomical structures
30773	30773	SRR28348939	SRX23954957	SRS20755378	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 Embryo 0hpf rep2	GSM8147854	source name:Whole embryo\|tissue:Whole embryo\|developmental stage:0hpf\|genotype:AB TF and TLF\|geo loc name:missing\|collection date:missing	Zebrafish Embryo 0hpf 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	Whole embryo		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:Whole embryo\|developmental stage:0hpf\|genotype:AB TF and TLF	GSM8147854	GSM8147854: Zebrafish Embryo 0hpf rep2; Danio rerio; RNA Seq	GSM8147854 r1	GSM8147854	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		s_0hpf_2.fastq	fastq	1775936764.0	23367589.0	GSM8147854 r1	0:76	A:430534781;C:442757587;G:423062009;T:479501608;N:80779	76		430534781	442757587	423062009	479501608	80779	SRX23954957	SRS20755378	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	Zygote	Embryo	Whole Organism	All anatomical structures
30774	30774	SRR28348940	SRX23954956	SRS20755377	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 Embryo 0hpf rep1	GSM8147853	source name:Whole embryo\|tissue:Whole embryo\|developmental stage:0hpf\|genotype:AB TF and TLF\|geo loc name:missing\|collection date:missing	Zebrafish Embryo 0hpf 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	Whole embryo		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:Whole embryo\|developmental stage:0hpf\|genotype:AB TF and TLF	GSM8147853	GSM8147853: Zebrafish Embryo 0hpf rep1; Danio rerio; RNA Seq	GSM8147853 r1	GSM8147853	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		s_0hpf_1.fastq	fastq	1616867016.0	21274566.0	GSM8147853 r1	0:76	A:390223732;C:404962813;G:373130983;T:448474905;N:74583	76		390223732	404962813	373130983	448474905	74583	SRX23954956	SRS20755377	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	Zygote	Embryo	Whole Organism	All anatomical structures
41442	41442	SRR4423757	SRX2245918	SRS1746324	SRP091576	PRJNA348537	Polysome seq in zebrafish early embryonic development	GSE88776	Transcriptome Analysis	We followed the polysomal association of maternal and early zygotic transcriptome over the first few hours of embryonic development prior to and post MBT. We isolated polysome associated bound and non polysome associated unbound mRNAs using sucrose gradient centrifugation followed by size fractionation. Using next generation sequencing RNA seq we profiled the transcriptome in polysome bound and unbound fractions. Our analysis revealed distinct dynamics of polysome association of cytoplasmically polyadenylated maternal mRNAs. Overall design: rRNA depleted RNA was extracted from pooled embryos of desired stages Egg 1 cell 16 cells 128 cells 3.5hpf and 5.3hpf and subjected to polysome profiling to separate between polysome free and polysome associated fragments. Unfractionated rRNA depleted samples at corresponding stages were used as background control. One RNA seq library was generated for each sample.		pubmed:29229769		1 cell unfractionated	GSM2345440	source name:whole zebrafish embryo\|strain:wild type AB\|developmental stage:1cell\|tissue:whole embryo	1 cell unfractionated	Basecalling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10. For the RNA Seq data analysis sequencing reads were aligned to the GRCz10 zebrafish genome using STAR v2.4.2a Dobin et al. 2012. For the novel transcript discovery sequencing reads were trimmed using cutadapt 1.9.1 e 0.1; q 20; O 3; m 20; a AGATCGGAAGAGC. Subsequently the reads were aligned to the GRCz10 zebrafish genome using GSNAP version 2015 12 31 filter chastity=both; max mismatches=5; novelsplicing=1. Transcriptome was assembled using cufflinks 2.2.1 multi read correct; library type fr secondstrand with Ensembl release 83 genome annotation. Cuffcompare was run to compare and annotate the newly assembled transcripts. Transcript level abundances were generated using Salmon 0.6.0 algorithm Patro et al. 2015. The abundances were summarized to gene level and imported to DESeq2 using tximport 1.0.2. Subsequently data was normalized to library size using DESeq2 „median ratio method” Anders and Huber 2010. Genome build: GRCz10 Supplementary files format and content: Salmon's quantification files tab delimited text files contain abundance measurements for each sample. normalizedCounts.txt tab delimited text file contains counts for all the samples normalized using DESeq2.	whole zebrafish embryo		rRNA depletion was performed using RiboZero Magnetic Gold Kit Epicentre unfractionated polysome associated and non associated RNA were subsequently isolated using Qiagen RNAeasy kit Qiagen USA. Sequencing library was constructed using Stranded RNA seq libraries were generated using ScriptSeq v2 RNA Library Preparation Kit Illumina USA.	Zebrafish embryos were maintained according to standard protocol Westerfield et al. 2000 and staged according to standard morphological criteria Kimmel et al. 1995.	strain:wild type AB\|developmental stage:1cell\|tissue:whole embryo	GSM2345440	GSM2345440: 1 cell unfractionated; Danio rerio; RNA Seq	GSM2345440		1	rRNA depletion was performed using RiboZero Magnetic Gold Kit Epicentre unfractionated polysome associated and non associated RNA were subsequently isolated using Qiagen RNAeasy kit Qiagen USA. Sequencing library was constructed using Stranded RNA seq libraries were generated using ScriptSeq v2 RNA Library Preparation Kit Illumina USA.	GEO Accession:GSM2345440	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP091576		total_1Cell.fq.gz	fastq	3439185825.0	45855811.0	GSM2345440 r1	0:75	A:964800703;C:744893686;G:902196147;T:827012209;N:283080	75		964800703	744893686	902196147	827012209	283080	SRX2245918	SRS1746324	SRA485192	GEO	Laboratory of Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw	1	0.86668		0.08217		0.75043		0.48997		75		B		usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	Poland	2016-10-14	Zygote	Embryo	Whole Organism	All anatomical structures
41449	41449	SRR4423750	SRX2245912	SRS1746318	SRP091576	PRJNA348537	Polysome seq in zebrafish early embryonic development	GSE88776	Transcriptome Analysis	We followed the polysomal association of maternal and early zygotic transcriptome over the first few hours of embryonic development prior to and post MBT. We isolated polysome associated bound and non polysome associated unbound mRNAs using sucrose gradient centrifugation followed by size fractionation. Using next generation sequencing RNA seq we profiled the transcriptome in polysome bound and unbound fractions. Our analysis revealed distinct dynamics of polysome association of cytoplasmically polyadenylated maternal mRNAs. Overall design: rRNA depleted RNA was extracted from pooled embryos of desired stages Egg 1 cell 16 cells 128 cells 3.5hpf and 5.3hpf and subjected to polysome profiling to separate between polysome free and polysome associated fragments. Unfractionated rRNA depleted samples at corresponding stages were used as background control. One RNA seq library was generated for each sample.		pubmed:29229769		1 cell polysome unbound	GSM2345434	source name:whole zebrafish embryo\|strain:wild type AB\|developmental stage:1cell\|tissue:whole embryo	1 cell polysome unbound	Basecalling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10. For the RNA Seq data analysis sequencing reads were aligned to the GRCz10 zebrafish genome using STAR v2.4.2a Dobin et al. 2012. For the novel transcript discovery sequencing reads were trimmed using cutadapt 1.9.1 e 0.1; q 20; O 3; m 20; a AGATCGGAAGAGC. Subsequently the reads were aligned to the GRCz10 zebrafish genome using GSNAP version 2015 12 31 filter chastity=both; max mismatches=5; novelsplicing=1. Transcriptome was assembled using cufflinks 2.2.1 multi read correct; library type fr secondstrand with Ensembl release 83 genome annotation. Cuffcompare was run to compare and annotate the newly assembled transcripts. Transcript level abundances were generated using Salmon 0.6.0 algorithm Patro et al. 2015. The abundances were summarized to gene level and imported to DESeq2 using tximport 1.0.2. Subsequently data was normalized to library size using DESeq2 „median ratio method” Anders and Huber 2010. Genome build: GRCz10 Supplementary files format and content: Salmon's quantification files tab delimited text files contain abundance measurements for each sample. normalizedCounts.txt tab delimited text file contains counts for all the samples normalized using DESeq2.	whole zebrafish embryo		rRNA depletion was performed using RiboZero Magnetic Gold Kit Epicentre unfractionated polysome associated and non associated RNA were subsequently isolated using Qiagen RNAeasy kit Qiagen USA. Sequencing library was constructed using Stranded RNA seq libraries were generated using ScriptSeq v2 RNA Library Preparation Kit Illumina USA.	Zebrafish embryos were maintained according to standard protocol Westerfield et al. 2000 and staged according to standard morphological criteria Kimmel et al. 1995.	strain:wild type AB\|developmental stage:1cell\|tissue:whole embryo	GSM2345434	GSM2345434: 1 cell polysome unbound; Danio rerio; RNA Seq	GSM2345434		1	rRNA depletion was performed using RiboZero Magnetic Gold Kit Epicentre unfractionated polysome associated and non associated RNA were subsequently isolated using Qiagen RNAeasy kit Qiagen USA. Sequencing library was constructed using Stranded RNA seq libraries were generated using ScriptSeq v2 RNA Library Preparation Kit Illumina USA.	GEO Accession:GSM2345434	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP091576		unbound_1Cell.fq.gz	fastq	4132524225.0	55100323.0	GSM2345434 r1										SRX2245912	SRS1746318	SRA485192	GEO	Laboratory of Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw	1	0.83821		0.13815		0.75682		0.5164		75		B		usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	Poland	2016-10-14	Zygote	Embryo	Whole Organism	All anatomical structures
41455	41455	SRR4423744	SRX2245906	SRS1746312	SRP091576	PRJNA348537	Polysome seq in zebrafish early embryonic development	GSE88776	Transcriptome Analysis	We followed the polysomal association of maternal and early zygotic transcriptome over the first few hours of embryonic development prior to and post MBT. We isolated polysome associated bound and non polysome associated unbound mRNAs using sucrose gradient centrifugation followed by size fractionation. Using next generation sequencing RNA seq we profiled the transcriptome in polysome bound and unbound fractions. Our analysis revealed distinct dynamics of polysome association of cytoplasmically polyadenylated maternal mRNAs. Overall design: rRNA depleted RNA was extracted from pooled embryos of desired stages Egg 1 cell 16 cells 128 cells 3.5hpf and 5.3hpf and subjected to polysome profiling to separate between polysome free and polysome associated fragments. Unfractionated rRNA depleted samples at corresponding stages were used as background control. One RNA seq library was generated for each sample.		pubmed:29229769		1 cell polysome bound	GSM2345428	source name:whole zebrafish embryo\|strain:wild type AB\|developmental stage:1cell\|tissue:whole embryo	1 cell polysome bound	Basecalling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10. For the RNA Seq data analysis sequencing reads were aligned to the GRCz10 zebrafish genome using STAR v2.4.2a Dobin et al. 2012. For the novel transcript discovery sequencing reads were trimmed using cutadapt 1.9.1 e 0.1; q 20; O 3; m 20; a AGATCGGAAGAGC. Subsequently the reads were aligned to the GRCz10 zebrafish genome using GSNAP version 2015 12 31 filter chastity=both; max mismatches=5; novelsplicing=1. Transcriptome was assembled using cufflinks 2.2.1 multi read correct; library type fr secondstrand with Ensembl release 83 genome annotation. Cuffcompare was run to compare and annotate the newly assembled transcripts. Transcript level abundances were generated using Salmon 0.6.0 algorithm Patro et al. 2015. The abundances were summarized to gene level and imported to DESeq2 using tximport 1.0.2. Subsequently data was normalized to library size using DESeq2 „median ratio method” Anders and Huber 2010. Genome build: GRCz10 Supplementary files format and content: Salmon's quantification files tab delimited text files contain abundance measurements for each sample. normalizedCounts.txt tab delimited text file contains counts for all the samples normalized using DESeq2.	whole zebrafish embryo		rRNA depletion was performed using RiboZero Magnetic Gold Kit Epicentre unfractionated polysome associated and non associated RNA were subsequently isolated using Qiagen RNAeasy kit Qiagen USA. Sequencing library was constructed using Stranded RNA seq libraries were generated using ScriptSeq v2 RNA Library Preparation Kit Illumina USA.	Zebrafish embryos were maintained according to standard protocol Westerfield et al. 2000 and staged according to standard morphological criteria Kimmel et al. 1995.	strain:wild type AB\|developmental stage:1cell\|tissue:whole embryo	GSM2345428	GSM2345428: 1 cell polysome bound; Danio rerio; RNA Seq	GSM2345428		1	rRNA depletion was performed using RiboZero Magnetic Gold Kit Epicentre unfractionated polysome associated and non associated RNA were subsequently isolated using Qiagen RNAeasy kit Qiagen USA. Sequencing library was constructed using Stranded RNA seq libraries were generated using ScriptSeq v2 RNA Library Preparation Kit Illumina USA.	GEO Accession:GSM2345428	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP091576		bound_1Cell.fq.gz	fastq	5536748025.0	73823307.0	GSM2345428 r1	0:75	A:1575347291;C:1208666132;G:1460599029;T:1291780516;N:355057	75		1575347291	1208666132	1460599029	1291780516	355057	SRX2245906	SRS1746312	SRA485192	GEO	Laboratory of Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology in Warsaw	1	0.89822		0.04829		0.77869		0.46794		75		B		usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	Poland	2016-10-14	Zygote	Embryo	Whole Organism	All anatomical structures
49147	49147	SRR9962809	SRX6710338	SRS5264193	SRP158893	PRJNA488043	Loss of maternal and zygotic ezh2 reveals the function of Polycomb repression in maintenance of gene expression domain post the body plan is established in zebrafish	GSE119070	Other	The goal of the ChIP sequencing experiments was to assess the differences in occupancy of a selection of chromatin marks and chromatin associated proteins in absence of both maternal and zygotic Ezh2 in zebrafish embryos at 24 hpf. The goal of RNA sequencing experiments was to ass the effect of the absence of both maternal and zygotic Ezh2 on gene expression in zebrafish embryos at 0 3.3 and 24 hpf and link these differences with the changes in epigenetic mark occupancy. Overall design: RNAseq of 0 hph 3.3hpf and 24 hpf Danio rerio wildtype and maternal zygotic ezh2 MZezh2 mutant whole embyos 5 to 7 replicates; ChIPseq for Ezh2 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos both second replicates Drosophila spike in chromatin was used to assess ChIP and library quality; ChIPseq for H3K27me3 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos both second replicates Drosophila spike in chromatin was used to assess ChIP and library quality; ChIPseq for Rnf2 in 24 hpf Danio rerio wildtype 1 replicates and MZezh2 mutant 2 sample whole embryos; ChIPseq for H3K4me3 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos; ChIPseq for H3K27ac in 24 hpf Danio rerio wildtype 3 replicates and MZezh2 mutant 3 sample whole embryos;		pubmed:31488564		RNAseq MZezh2mutant 0hpf rep6	GSM4030411	tissue:RNAseq MZezh2mutant 0hpf\|strain background:TU/TLF mixed background\|genotype/variation:MZezh2 / \|age:0 hpf embryo	RNAseq MZezh2mutant 0hpf rep6	RNA seq: reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Genome build: GRCz10 Supplementary files format and content: Raw gene counts .tab	RNAseq MZezh2mutant 0hpf		RNA seq: Embryos of 24 hpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit. RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation.	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain background:TU/TLF mixed background\|genotype/variation:MZezh2 / \|age:0 hpf embryo	GSM4030411	GSM4030411: RNAseq MZezh2mutant 0hpf rep6; Danio rerio; RNA Seq	GSM4030411		1	RNA seq: Embryos of 24 hpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit. RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP158893		RNAseq_MZezh2mutant_0hpf_rep6_R1.fastq.gz RNAseq_MZezh2mutant_0hpf_rep6_R2.fastq.gz	fastq fastq	1818269208.0	21646062.0	GSM4030411 r1	0:42 1:42	A:467737566;C:434429557;G:451696449;T:463995685;N:409951	42	42	467737566	434429557	451696449	463995685	409951	SRX6710338	SRS5264193	SRA763417	GEO	Molecular Biology, Radboud University	2	0.63664	0.64501	0.1054	0.101	0.73736	0.73937	0.47347	0.47482	42	42	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	Netherlands	2019-08-13	Zygote	Embryo	Whole Organism	All anatomical structures
49148	49148	SRR9962808	SRX6710337	SRS5264192	SRP158893	PRJNA488043	Loss of maternal and zygotic ezh2 reveals the function of Polycomb repression in maintenance of gene expression domain post the body plan is established in zebrafish	GSE119070	Other	The goal of the ChIP sequencing experiments was to assess the differences in occupancy of a selection of chromatin marks and chromatin associated proteins in absence of both maternal and zygotic Ezh2 in zebrafish embryos at 24 hpf. The goal of RNA sequencing experiments was to ass the effect of the absence of both maternal and zygotic Ezh2 on gene expression in zebrafish embryos at 0 3.3 and 24 hpf and link these differences with the changes in epigenetic mark occupancy. Overall design: RNAseq of 0 hph 3.3hpf and 24 hpf Danio rerio wildtype and maternal zygotic ezh2 MZezh2 mutant whole embyos 5 to 7 replicates; ChIPseq for Ezh2 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos both second replicates Drosophila spike in chromatin was used to assess ChIP and library quality; ChIPseq for H3K27me3 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos both second replicates Drosophila spike in chromatin was used to assess ChIP and library quality; ChIPseq for Rnf2 in 24 hpf Danio rerio wildtype 1 replicates and MZezh2 mutant 2 sample whole embryos; ChIPseq for H3K4me3 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos; ChIPseq for H3K27ac in 24 hpf Danio rerio wildtype 3 replicates and MZezh2 mutant 3 sample whole embryos;		pubmed:31488564		RNAseq MZezh2mutant 0hpf rep5	GSM4030410	tissue:RNAseq MZezh2mutant 0hpf\|strain background:TU/TLF mixed background\|genotype/variation:MZezh2 / \|age:0 hpf embryo	RNAseq MZezh2mutant 0hpf rep5	RNA seq: reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Genome build: GRCz10 Supplementary files format and content: Raw gene counts .tab	RNAseq MZezh2mutant 0hpf		RNA seq: Embryos of 24 hpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit. RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation.	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain background:TU/TLF mixed background\|genotype/variation:MZezh2 / \|age:0 hpf embryo	GSM4030410	GSM4030410: RNAseq MZezh2mutant 0hpf rep5; Danio rerio; RNA Seq	GSM4030410		1	RNA seq: Embryos of 24 hpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit. RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP158893		RNAseq_MZezh2mutant_0hpf_rep5_R1.fastq.gz RNAseq_MZezh2mutant_0hpf_rep5_R2.fastq.gz	fastq fastq	1309683312.0	15591468.0	GSM4030410 r1	0:42 1:42	A:329502612;C:318644310;G:333025741;T:328212129;N:298520	42	42	329502612	318644310	333025741	328212129	298520	SRX6710337	SRS5264192	SRA763417	GEO	Molecular Biology, Radboud University	2	0.65763	0.66663	0.0995	0.09643	0.73618	0.73768	0.47844	0.47578	42	42	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	Netherlands	2019-08-13	Zygote	Embryo	Whole Organism	All anatomical structures
49149	49149	SRR9962807	SRX6710336	SRS5264191	SRP158893	PRJNA488043	Loss of maternal and zygotic ezh2 reveals the function of Polycomb repression in maintenance of gene expression domain post the body plan is established in zebrafish	GSE119070	Other	The goal of the ChIP sequencing experiments was to assess the differences in occupancy of a selection of chromatin marks and chromatin associated proteins in absence of both maternal and zygotic Ezh2 in zebrafish embryos at 24 hpf. The goal of RNA sequencing experiments was to ass the effect of the absence of both maternal and zygotic Ezh2 on gene expression in zebrafish embryos at 0 3.3 and 24 hpf and link these differences with the changes in epigenetic mark occupancy. Overall design: RNAseq of 0 hph 3.3hpf and 24 hpf Danio rerio wildtype and maternal zygotic ezh2 MZezh2 mutant whole embyos 5 to 7 replicates; ChIPseq for Ezh2 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos both second replicates Drosophila spike in chromatin was used to assess ChIP and library quality; ChIPseq for H3K27me3 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos both second replicates Drosophila spike in chromatin was used to assess ChIP and library quality; ChIPseq for Rnf2 in 24 hpf Danio rerio wildtype 1 replicates and MZezh2 mutant 2 sample whole embryos; ChIPseq for H3K4me3 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos; ChIPseq for H3K27ac in 24 hpf Danio rerio wildtype 3 replicates and MZezh2 mutant 3 sample whole embryos;		pubmed:31488564		RNAseq MZezh2mutant 0hpf rep4	GSM4030409	tissue:RNAseq MZezh2mutant 0hpf\|strain background:TU/TLF mixed background\|genotype/variation:MZezh2 / \|age:0 hpf embryo	RNAseq MZezh2mutant 0hpf rep4	RNA seq: reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Genome build: GRCz10 Supplementary files format and content: Raw gene counts .tab	RNAseq MZezh2mutant 0hpf		RNA seq: Embryos of 24 hpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit. RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation.	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain background:TU/TLF mixed background\|genotype/variation:MZezh2 / \|age:0 hpf embryo	GSM4030409	GSM4030409: RNAseq MZezh2mutant 0hpf rep4; Danio rerio; RNA Seq	GSM4030409		1	RNA seq: Embryos of 24 hpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit. RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP158893		RNAseq_MZezh2mutant_0hpf_rep4_R1.fastq.gz RNAseq_MZezh2mutant_0hpf_rep4_R2.fastq.gz	fastq fastq	1215294948.0	14467797.0	GSM4030409 r1	0:42 1:42	A:267633749;C:328219619;G:347873253;T:271414174;N:154153	42	42	267633749	328219619	347873253	271414174	154153	SRX6710336	SRS5264191	SRA763417	GEO	Molecular Biology, Radboud University	2	0.60174	0.60326	0.04853	0.04743	0.7483	0.75091	0.47671	0.47718	42	42	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	Netherlands	2019-08-13	Zygote	Embryo	Whole Organism	All anatomical structures
49150	49150	SRR9962806	SRX6710335	SRS5264190	SRP158893	PRJNA488043	Loss of maternal and zygotic ezh2 reveals the function of Polycomb repression in maintenance of gene expression domain post the body plan is established in zebrafish	GSE119070	Other	The goal of the ChIP sequencing experiments was to assess the differences in occupancy of a selection of chromatin marks and chromatin associated proteins in absence of both maternal and zygotic Ezh2 in zebrafish embryos at 24 hpf. The goal of RNA sequencing experiments was to ass the effect of the absence of both maternal and zygotic Ezh2 on gene expression in zebrafish embryos at 0 3.3 and 24 hpf and link these differences with the changes in epigenetic mark occupancy. Overall design: RNAseq of 0 hph 3.3hpf and 24 hpf Danio rerio wildtype and maternal zygotic ezh2 MZezh2 mutant whole embyos 5 to 7 replicates; ChIPseq for Ezh2 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos both second replicates Drosophila spike in chromatin was used to assess ChIP and library quality; ChIPseq for H3K27me3 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos both second replicates Drosophila spike in chromatin was used to assess ChIP and library quality; ChIPseq for Rnf2 in 24 hpf Danio rerio wildtype 1 replicates and MZezh2 mutant 2 sample whole embryos; ChIPseq for H3K4me3 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos; ChIPseq for H3K27ac in 24 hpf Danio rerio wildtype 3 replicates and MZezh2 mutant 3 sample whole embryos;		pubmed:31488564		RNAseq MZezh2mutant 0hpf rep3	GSM4030408	tissue:RNAseq MZezh2mutant 0hpf\|strain background:TU/TLF mixed background\|genotype/variation:MZezh2 / \|age:0 hpf embryo	RNAseq MZezh2mutant 0hpf rep3	RNA seq: reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Genome build: GRCz10 Supplementary files format and content: Raw gene counts .tab	RNAseq MZezh2mutant 0hpf		RNA seq: Embryos of 24 hpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit. RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation.	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain background:TU/TLF mixed background\|genotype/variation:MZezh2 / \|age:0 hpf embryo	GSM4030408	GSM4030408: RNAseq MZezh2mutant 0hpf rep3; Danio rerio; RNA Seq	GSM4030408		1	RNA seq: Embryos of 24 hpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit. RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP158893		RNAseq_MZezh2mutant_0hpf_rep3_R1.fastq.gz RNAseq_MZezh2mutant_0hpf_rep3_R2.fastq.gz	fastq fastq	1622530896.0	19315844.0	GSM4030408 r1	0:42 1:42	A:440097761;C:363961944;G:379239276;T:438866006;N:365909	42	42	440097761	363961944	379239276	438866006	365909	SRX6710335	SRS5264190	SRA763417	GEO	Molecular Biology, Radboud University	2	0.65981	0.6685	0.09588	0.09403	0.74428	0.74696	0.49188	0.49675	42	42	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	Netherlands	2019-08-13	Zygote	Embryo	Whole Organism	All anatomical structures
49151	49151	SRR9962803	SRX6710332	SRS5264187	SRP158893	PRJNA488043	Loss of maternal and zygotic ezh2 reveals the function of Polycomb repression in maintenance of gene expression domain post the body plan is established in zebrafish	GSE119070	Other	The goal of the ChIP sequencing experiments was to assess the differences in occupancy of a selection of chromatin marks and chromatin associated proteins in absence of both maternal and zygotic Ezh2 in zebrafish embryos at 24 hpf. The goal of RNA sequencing experiments was to ass the effect of the absence of both maternal and zygotic Ezh2 on gene expression in zebrafish embryos at 0 3.3 and 24 hpf and link these differences with the changes in epigenetic mark occupancy. Overall design: RNAseq of 0 hph 3.3hpf and 24 hpf Danio rerio wildtype and maternal zygotic ezh2 MZezh2 mutant whole embyos 5 to 7 replicates; ChIPseq for Ezh2 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos both second replicates Drosophila spike in chromatin was used to assess ChIP and library quality; ChIPseq for H3K27me3 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos both second replicates Drosophila spike in chromatin was used to assess ChIP and library quality; ChIPseq for Rnf2 in 24 hpf Danio rerio wildtype 1 replicates and MZezh2 mutant 2 sample whole embryos; ChIPseq for H3K4me3 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos; ChIPseq for H3K27ac in 24 hpf Danio rerio wildtype 3 replicates and MZezh2 mutant 3 sample whole embryos;		pubmed:31488564		RNAseq Wildtype 0hpf rep5	GSM4030405	tissue:RNAseq Wildtype 0hpf\|strain background:TU/TLF mixed background\|genotype/variation:wildtype\|age:0 hpf embryo	RNAseq Wildtype 0hpf rep5	RNA seq: reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Genome build: GRCz10 Supplementary files format and content: Raw gene counts .tab	RNAseq Wildtype 0hpf		RNA seq: Embryos of 24 hpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit. RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation.	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain background:TU/TLF mixed background\|genotype/variation:wildtype\|age:0 hpf embryo	GSM4030405	GSM4030405: RNAseq Wildtype 0hpf rep5; Danio rerio; RNA Seq	GSM4030405		1	RNA seq: Embryos of 24 hpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit. RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP158893		RNAseq_Wildtype_0hpf_rep5_R1.fastq.gz RNAseq_Wildtype_0hpf_rep5_R2.fastq.gz	fastq fastq	1805412504.0	21493006.0	GSM4030405 r1	0:42 1:42	A:457244338;C:429898081;G:467819503;T:450049480;N:401102	42	42	457244338	429898081	467819503	450049480	401102	SRX6710332	SRS5264187	SRA763417	GEO	Molecular Biology, Radboud University	2	0.78367	0.79205	0.08838	0.08821	0.74042	0.74326	0.47967	0.47669	42	42	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	Netherlands	2019-08-13	Zygote	Embryo	Whole Organism	All anatomical structures
49152	49152	SRR9962802	SRX6710331	SRS5264186	SRP158893	PRJNA488043	Loss of maternal and zygotic ezh2 reveals the function of Polycomb repression in maintenance of gene expression domain post the body plan is established in zebrafish	GSE119070	Other	The goal of the ChIP sequencing experiments was to assess the differences in occupancy of a selection of chromatin marks and chromatin associated proteins in absence of both maternal and zygotic Ezh2 in zebrafish embryos at 24 hpf. The goal of RNA sequencing experiments was to ass the effect of the absence of both maternal and zygotic Ezh2 on gene expression in zebrafish embryos at 0 3.3 and 24 hpf and link these differences with the changes in epigenetic mark occupancy. Overall design: RNAseq of 0 hph 3.3hpf and 24 hpf Danio rerio wildtype and maternal zygotic ezh2 MZezh2 mutant whole embyos 5 to 7 replicates; ChIPseq for Ezh2 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos both second replicates Drosophila spike in chromatin was used to assess ChIP and library quality; ChIPseq for H3K27me3 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos both second replicates Drosophila spike in chromatin was used to assess ChIP and library quality; ChIPseq for Rnf2 in 24 hpf Danio rerio wildtype 1 replicates and MZezh2 mutant 2 sample whole embryos; ChIPseq for H3K4me3 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos; ChIPseq for H3K27ac in 24 hpf Danio rerio wildtype 3 replicates and MZezh2 mutant 3 sample whole embryos;		pubmed:31488564		RNAseq Wildtype 0hpf rep4	GSM4030404	tissue:RNAseq Wildtype 0hpf\|strain background:TU/TLF mixed background\|genotype/variation:wildtype\|age:0 hpf embryo	RNAseq Wildtype 0hpf rep4	RNA seq: reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Genome build: GRCz10 Supplementary files format and content: Raw gene counts .tab	RNAseq Wildtype 0hpf		RNA seq: Embryos of 24 hpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit. RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation.	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain background:TU/TLF mixed background\|genotype/variation:wildtype\|age:0 hpf embryo	GSM4030404	GSM4030404: RNAseq Wildtype 0hpf rep4; Danio rerio; RNA Seq	GSM4030404		1	RNA seq: Embryos of 24 hpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit. RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP158893		RNAseq_Wildtype_0hpf_rep4_R1.fastq.gz RNAseq_Wildtype_0hpf_rep4_R2.fastq.gz	fastq fastq	1939354284.0	23087551.0	GSM4030404 r1	0:42 1:42	A:514773605;C:443939765;G:469903130;T:510299249;N:438535	42	42	514773605	443939765	469903130	510299249	438535	SRX6710331	SRS5264186	SRA763417	GEO	Molecular Biology, Radboud University	2	0.76942	0.78086	0.08315	0.07992	0.74499	0.74588	0.47955	0.47941	42	42	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	Netherlands	2019-08-13	Zygote	Embryo	Whole Organism	All anatomical structures
49153	49153	SRR9962801	SRX6710330	SRS5264185	SRP158893	PRJNA488043	Loss of maternal and zygotic ezh2 reveals the function of Polycomb repression in maintenance of gene expression domain post the body plan is established in zebrafish	GSE119070	Other	The goal of the ChIP sequencing experiments was to assess the differences in occupancy of a selection of chromatin marks and chromatin associated proteins in absence of both maternal and zygotic Ezh2 in zebrafish embryos at 24 hpf. The goal of RNA sequencing experiments was to ass the effect of the absence of both maternal and zygotic Ezh2 on gene expression in zebrafish embryos at 0 3.3 and 24 hpf and link these differences with the changes in epigenetic mark occupancy. Overall design: RNAseq of 0 hph 3.3hpf and 24 hpf Danio rerio wildtype and maternal zygotic ezh2 MZezh2 mutant whole embyos 5 to 7 replicates; ChIPseq for Ezh2 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos both second replicates Drosophila spike in chromatin was used to assess ChIP and library quality; ChIPseq for H3K27me3 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos both second replicates Drosophila spike in chromatin was used to assess ChIP and library quality; ChIPseq for Rnf2 in 24 hpf Danio rerio wildtype 1 replicates and MZezh2 mutant 2 sample whole embryos; ChIPseq for H3K4me3 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos; ChIPseq for H3K27ac in 24 hpf Danio rerio wildtype 3 replicates and MZezh2 mutant 3 sample whole embryos;		pubmed:31488564		RNAseq Wildtype 0hpf rep3	GSM4030403	tissue:RNAseq Wildtype 0hpf\|strain background:TU/TLF mixed background\|genotype/variation:wildtype\|age:0 hpf embryo	RNAseq Wildtype 0hpf rep3	RNA seq: reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Genome build: GRCz10 Supplementary files format and content: Raw gene counts .tab	RNAseq Wildtype 0hpf		RNA seq: Embryos of 24 hpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit. RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation.	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain background:TU/TLF mixed background\|genotype/variation:wildtype\|age:0 hpf embryo	GSM4030403	GSM4030403: RNAseq Wildtype 0hpf rep3; Danio rerio; RNA Seq	GSM4030403		1	RNA seq: Embryos of 24 hpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit. RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP158893		RNAseq_Wildtype_0hpf_rep3_R1.fastq.gz RNAseq_Wildtype_0hpf_rep3_R2.fastq.gz	fastq fastq	2177720496.0	25925244.0	GSM4030403 r1	0:42 1:42	A:729069077;C:343146233;G:387147512;T:717858484;N:499190	42	42	729069077	343146233	387147512	717858484	499190	SRX6710330	SRS5264185	SRA763417	GEO	Molecular Biology, Radboud University	2	0.36691	0.38913	0.04711	0.05153	0.80383	0.80616	0.47587	0.47907	42	42	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	Netherlands	2019-08-13	Zygote	Embryo	Whole Organism	All anatomical structures
49158	49158	SRR9962805	SRX6710334	SRS5264189	SRP158893	PRJNA488043	Loss of maternal and zygotic ezh2 reveals the function of Polycomb repression in maintenance of gene expression domain post the body plan is established in zebrafish	GSE119070	Other	The goal of the ChIP sequencing experiments was to assess the differences in occupancy of a selection of chromatin marks and chromatin associated proteins in absence of both maternal and zygotic Ezh2 in zebrafish embryos at 24 hpf. The goal of RNA sequencing experiments was to ass the effect of the absence of both maternal and zygotic Ezh2 on gene expression in zebrafish embryos at 0 3.3 and 24 hpf and link these differences with the changes in epigenetic mark occupancy. Overall design: RNAseq of 0 hph 3.3hpf and 24 hpf Danio rerio wildtype and maternal zygotic ezh2 MZezh2 mutant whole embyos 5 to 7 replicates; ChIPseq for Ezh2 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos both second replicates Drosophila spike in chromatin was used to assess ChIP and library quality; ChIPseq for H3K27me3 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos both second replicates Drosophila spike in chromatin was used to assess ChIP and library quality; ChIPseq for Rnf2 in 24 hpf Danio rerio wildtype 1 replicates and MZezh2 mutant 2 sample whole embryos; ChIPseq for H3K4me3 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos; ChIPseq for H3K27ac in 24 hpf Danio rerio wildtype 3 replicates and MZezh2 mutant 3 sample whole embryos;		pubmed:31488564		RNAseq MZezh2mutant 0hpf rep2	GSM4030407	tissue:RNAseq MZezh2mutant 0hpf\|strain background:TU/TLF mixed background\|genotype/variation:MZezh2 / \|age:0 hpf embryo	RNAseq MZezh2mutant 0hpf rep2	RNA seq: reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Genome build: GRCz10 Supplementary files format and content: Raw gene counts .tab	RNAseq MZezh2mutant 0hpf		RNA seq: Embryos of 24 hpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit. RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation.	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain background:TU/TLF mixed background\|genotype/variation:MZezh2 / \|age:0 hpf embryo	GSM4030407	GSM4030407: RNAseq MZezh2mutant 0hpf rep2; Danio rerio; RNA Seq	GSM4030407		1	RNA seq: Embryos of 24 hpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit. RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation.	GEO Accession:GSM4030407	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP158893		RNAseq_MZezh2mutant_0hpf_rep2.fastq.gz	fastq	1547722600.0	30954452.0	GSM4030407 r1	0:50	A:328831606;C:407052662;G:414676558;T:396893106;N:268668	50		328831606	407052662	414676558	396893106	268668	SRX6710334	SRS5264189	SRA763417	GEO	Molecular Biology, Radboud University	1	0.86797		0.04692		0.72389		0.50852		50		B		usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	Netherlands	2019-08-13	Zygote	Embryo	Whole Organism	All anatomical structures
49159	49159	SRR9962804	SRX6710333	SRS5264188	SRP158893	PRJNA488043	Loss of maternal and zygotic ezh2 reveals the function of Polycomb repression in maintenance of gene expression domain post the body plan is established in zebrafish	GSE119070	Other	The goal of the ChIP sequencing experiments was to assess the differences in occupancy of a selection of chromatin marks and chromatin associated proteins in absence of both maternal and zygotic Ezh2 in zebrafish embryos at 24 hpf. The goal of RNA sequencing experiments was to ass the effect of the absence of both maternal and zygotic Ezh2 on gene expression in zebrafish embryos at 0 3.3 and 24 hpf and link these differences with the changes in epigenetic mark occupancy. Overall design: RNAseq of 0 hph 3.3hpf and 24 hpf Danio rerio wildtype and maternal zygotic ezh2 MZezh2 mutant whole embyos 5 to 7 replicates; ChIPseq for Ezh2 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos both second replicates Drosophila spike in chromatin was used to assess ChIP and library quality; ChIPseq for H3K27me3 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos both second replicates Drosophila spike in chromatin was used to assess ChIP and library quality; ChIPseq for Rnf2 in 24 hpf Danio rerio wildtype 1 replicates and MZezh2 mutant 2 sample whole embryos; ChIPseq for H3K4me3 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos; ChIPseq for H3K27ac in 24 hpf Danio rerio wildtype 3 replicates and MZezh2 mutant 3 sample whole embryos;		pubmed:31488564		RNAseq MZezh2mutant 0hpf rep1	GSM4030406	tissue:RNAseq MZezh2mutant 0hpf\|strain background:TU/TLF mixed background\|genotype/variation:MZezh2 / \|age:0 hpf embryo	RNAseq MZezh2mutant 0hpf rep1	RNA seq: reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Genome build: GRCz10 Supplementary files format and content: Raw gene counts .tab	RNAseq MZezh2mutant 0hpf		RNA seq: Embryos of 24 hpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit. RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation.	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain background:TU/TLF mixed background\|genotype/variation:MZezh2 / \|age:0 hpf embryo	GSM4030406	GSM4030406: RNAseq MZezh2mutant 0hpf rep1; Danio rerio; RNA Seq	GSM4030406		1	RNA seq: Embryos of 24 hpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit. RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation.	GEO Accession:GSM4030406	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP158893		RNAseq_MZezh2mutant_0hpf_rep1.fastq.gz	fastq	1605186150.0	32103723.0	GSM4030406 r1	0:50	A:349080671;C:422663752;G:408083708;T:424500446;N:857573	50		349080671	422663752	408083708	424500446	857573	SRX6710333	SRS5264188	SRA763417	GEO	Molecular Biology, Radboud University	1	0.87792		0.06048		0.73764		0.54181		50		B		usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	Netherlands	2019-08-13	Zygote	Embryo	Whole Organism	All anatomical structures
49160	49160	SRR9962800	SRX6710329	SRS5264184	SRP158893	PRJNA488043	Loss of maternal and zygotic ezh2 reveals the function of Polycomb repression in maintenance of gene expression domain post the body plan is established in zebrafish	GSE119070	Other	The goal of the ChIP sequencing experiments was to assess the differences in occupancy of a selection of chromatin marks and chromatin associated proteins in absence of both maternal and zygotic Ezh2 in zebrafish embryos at 24 hpf. The goal of RNA sequencing experiments was to ass the effect of the absence of both maternal and zygotic Ezh2 on gene expression in zebrafish embryos at 0 3.3 and 24 hpf and link these differences with the changes in epigenetic mark occupancy. Overall design: RNAseq of 0 hph 3.3hpf and 24 hpf Danio rerio wildtype and maternal zygotic ezh2 MZezh2 mutant whole embyos 5 to 7 replicates; ChIPseq for Ezh2 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos both second replicates Drosophila spike in chromatin was used to assess ChIP and library quality; ChIPseq for H3K27me3 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos both second replicates Drosophila spike in chromatin was used to assess ChIP and library quality; ChIPseq for Rnf2 in 24 hpf Danio rerio wildtype 1 replicates and MZezh2 mutant 2 sample whole embryos; ChIPseq for H3K4me3 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos; ChIPseq for H3K27ac in 24 hpf Danio rerio wildtype 3 replicates and MZezh2 mutant 3 sample whole embryos;		pubmed:31488564		RNAseq Wildtype 0hpf rep2	GSM4030402	tissue:RNAseq Wildtype 0hpf\|strain background:TU/TLF mixed background\|genotype/variation:wildtype\|age:0 hpf embryo	RNAseq Wildtype 0hpf rep2	RNA seq: reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Genome build: GRCz10 Supplementary files format and content: Raw gene counts .tab	RNAseq Wildtype 0hpf		RNA seq: Embryos of 24 hpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit. RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation.	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain background:TU/TLF mixed background\|genotype/variation:wildtype\|age:0 hpf embryo	GSM4030402	GSM4030402: RNAseq Wildtype 0hpf rep2; Danio rerio; RNA Seq	GSM4030402		1	RNA seq: Embryos of 24 hpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit. RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation.	GEO Accession:GSM4030402	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP158893		RNAseq_Wildtype_0hpf_rep2.fastq.gz	fastq	1598223000.0	31964460.0	GSM4030402 r1	0:50	A:363625463;C:410104847;G:395688370;T:428524090;N:280230	50		363625463	410104847	395688370	428524090	280230	SRX6710329	SRS5264184	SRA763417	GEO	Molecular Biology, Radboud University	1	0.9258		0.07165		0.74761		0.53094		50		B		usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	Netherlands	2019-08-13	Zygote	Embryo	Whole Organism	All anatomical structures
49161	49161	SRR9962799	SRX6710328	SRS5264183	SRP158893	PRJNA488043	Loss of maternal and zygotic ezh2 reveals the function of Polycomb repression in maintenance of gene expression domain post the body plan is established in zebrafish	GSE119070	Other	The goal of the ChIP sequencing experiments was to assess the differences in occupancy of a selection of chromatin marks and chromatin associated proteins in absence of both maternal and zygotic Ezh2 in zebrafish embryos at 24 hpf. The goal of RNA sequencing experiments was to ass the effect of the absence of both maternal and zygotic Ezh2 on gene expression in zebrafish embryos at 0 3.3 and 24 hpf and link these differences with the changes in epigenetic mark occupancy. Overall design: RNAseq of 0 hph 3.3hpf and 24 hpf Danio rerio wildtype and maternal zygotic ezh2 MZezh2 mutant whole embyos 5 to 7 replicates; ChIPseq for Ezh2 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos both second replicates Drosophila spike in chromatin was used to assess ChIP and library quality; ChIPseq for H3K27me3 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos both second replicates Drosophila spike in chromatin was used to assess ChIP and library quality; ChIPseq for Rnf2 in 24 hpf Danio rerio wildtype 1 replicates and MZezh2 mutant 2 sample whole embryos; ChIPseq for H3K4me3 in 24 hpf Danio rerio wildtype 2 replicates and MZezh2 mutant 2 sample whole embryos; ChIPseq for H3K27ac in 24 hpf Danio rerio wildtype 3 replicates and MZezh2 mutant 3 sample whole embryos;		pubmed:31488564		RNAseq Wildtype 0hpf rep1	GSM4030401	tissue:RNAseq Wildtype 0hpf\|strain background:TU/TLF mixed background\|genotype/variation:wildtype\|age:0 hpf embryo	RNAseq Wildtype 0hpf rep1	RNA seq: reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with quantMode geneCounts Genome build: GRCz10 Supplementary files format and content: Raw gene counts .tab	RNAseq Wildtype 0hpf		RNA seq: Embryos of 24 hpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit. RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation.	Zebrafish Danio rerio were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al. 1995.	strain background:TU/TLF mixed background\|genotype/variation:wildtype\|age:0 hpf embryo	GSM4030401	GSM4030401: RNAseq Wildtype 0hpf rep1; Danio rerio; RNA Seq	GSM4030401		1	RNA seq: Embryos of 24 hpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit. RNA seq: extraction was followed by fragmentation cDNA synthesis and KAPA HYPERprep library preparation.	GEO Accession:GSM4030401	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP158893		RNAseq_Wildtype_0hpf_rep1.fastq.gz	fastq	1559935850.0	31198717.0	GSM4030401 r1	0:50	A:341974228;C:412268833;G:394718567;T:410139637;N:834585	50		341974228	412268833	394718567	410139637	834585	SRX6710328	SRS5264183	SRA763417	GEO	Molecular Biology, Radboud University	1	0.86404		0.0655		0.75132		0.52527		50		B		usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	ribozero	bulk	unknown	unknown	Netherlands	2019-08-13	Zygote	Embryo	Whole Organism	All anatomical structures
49535	49535	SRR7942606	SRX4776871	SRS3857410	SRP162874	PRJNA493827	Transcriptomics analysis of gene expression in wide type ybx1 MO pabpc1a MO zebrafish embryo sample.	GSE120643	Other	The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of [1] gene expressive levels in wide type and ybx1 MO zebrafish embryo [2] gene expressive levels in pabpc1a MO zebrafish embryo [3] mRNA lifetime in wide type zebrafish embryo. Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol Reagent Ambion. mRNA was extracted with using Dynabeads mRNA Purification Kit Ambion and subjected to TURBO DNase Invitrogen treatment at 37C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA Seq library construction. Libraries were directly constructed using the KAPA Stranded mRNA Seq Kit KAPA and were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 125 bp. Synchronously developing embryos were treated with 0.2 ng of Pol II inhibition alpha amanitin Sigma at one cell stage and were collected at indicated time points. 100 embryos were collected for each time point in duplicates. The total RNA was extracted by Trizol…	parent bioproject:PRJNA534030			WT 0hpf rep2	GSM3406870	source name:Zebrafish embryo\|strain:AB strain\|cell type:Zebrafish embryo\|age:0 hpf\|tissue:whole embryo	WT 0hpf rep2	Reads were aligned to the zv9 genome assembly using TopHat v2.1.1 The number of reads mapped to each Ensemble gene was counted using the HTSeq v0.6.0 Genome build: zv9 Supplementary files format and content: Reads count for each gene in wild type ybx1 MO and pabpc1a MO sample	Zebrafish embryo		Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA Seq library construction. Libraries were directly constructed using the KAPA Stranded mRNA Seq Kit KAPA and were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 125 bp.		strain:AB strain\|cell type:Zebrafish embryo\|age:0 hpf\|tissue:whole embryo	GSM3406870	GSM3406870: WT 0hpf rep2; Danio rerio; RNA Seq	GSM3406870		1	Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA Seq library construction. Libraries were directly constructed using the KAPA Stranded mRNA Seq Kit KAPA and were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 125 bp.	GEO Accession:GSM3406870	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP162874	loader:latf load	WT_0hpf_rep2_R1.fastq.gz WT_0hpf_rep2_R2.fastq.gz	fastq fastq	9235008100.0	34013490.0	GSM3406870 r1	0:135.76 1:135.76	A:2585376157;C:2035534424;G:2087400121;T:2523389569;N:3307829	135	135	2585376157	2035534424	2087400121	2523389569	3307829	SRX4776871	SRS3857410	SRA786936	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.95881	0.96263	0.02093	0.01978	0.79121	0.79446	0.71203	0.33092	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	nebnext	bulk	unknown	unknown	China	2018-09-28	Zygote	Embryo	Whole Organism	All anatomical structures
49536	49536	SRR7942605	SRX4776870	SRS3857409	SRP162874	PRJNA493827	Transcriptomics analysis of gene expression in wide type ybx1 MO pabpc1a MO zebrafish embryo sample.	GSE120643	Other	The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of [1] gene expressive levels in wide type and ybx1 MO zebrafish embryo [2] gene expressive levels in pabpc1a MO zebrafish embryo [3] mRNA lifetime in wide type zebrafish embryo. Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol Reagent Ambion. mRNA was extracted with using Dynabeads mRNA Purification Kit Ambion and subjected to TURBO DNase Invitrogen treatment at 37C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA Seq library construction. Libraries were directly constructed using the KAPA Stranded mRNA Seq Kit KAPA and were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 125 bp. Synchronously developing embryos were treated with 0.2 ng of Pol II inhibition alpha amanitin Sigma at one cell stage and were collected at indicated time points. 100 embryos were collected for each time point in duplicates. The total RNA was extracted by Trizol…	parent bioproject:PRJNA534030			WT 0hpf rep1	GSM3406869	source name:Zebrafish embryo\|strain:AB strain\|cell type:Zebrafish embryo\|age:0 hpf\|tissue:whole embryo	WT 0hpf rep1	Reads were aligned to the zv9 genome assembly using TopHat v2.1.1 The number of reads mapped to each Ensemble gene was counted using the HTSeq v0.6.0 Genome build: zv9 Supplementary files format and content: Reads count for each gene in wild type ybx1 MO and pabpc1a MO sample	Zebrafish embryo		Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA Seq library construction. Libraries were directly constructed using the KAPA Stranded mRNA Seq Kit KAPA and were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 125 bp.		strain:AB strain\|cell type:Zebrafish embryo\|age:0 hpf\|tissue:whole embryo	GSM3406869	GSM3406869: WT 0hpf rep1; Danio rerio; RNA Seq	GSM3406869		1	Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA Seq library construction. Libraries were directly constructed using the KAPA Stranded mRNA Seq Kit KAPA and were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 125 bp.	GEO Accession:GSM3406869	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP162874	loader:latf load	WT_0hpf_rep1_R1.fastq.gz WT_0hpf_rep1_R2.fastq.gz	fastq fastq	14984219100.0	54916842.0	GSM3406869 r1	0:136.43 1:136.43	A:4170737129;C:3338746071;G:3400731292;T:4066538201;N:7466407	136	136	4170737129	3338746071	3400731292	4066538201	7466407	SRX4776870	SRS3857409	SRA786936	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.96613	0.96916	0.02325	0.02199	0.78758	0.79293	0.70396	0.7085	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	nebnext	bulk	unknown	unknown	China	2018-09-28	Zygote	Embryo	Whole Organism	All anatomical structures
49538	49538	SRR8937006	SRX5717519	SRS4655939	SRP162876	PRJNA493828	Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo sample.	GSE120646	Other	The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo. RIP seq: Briefly 500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl 10 mM HEPES pH 7.6 2 mM EDTA 0.5% NP 40 0.5 mM DTT 1:100 protease inhibitor cocktail 0.4 U/Î¼l RNasin by rotating at 4Â°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4Â°C for 1 h. 50 Î¼l pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax China and 30 Î¼l Protein A Dynabeads for 4 h at 4Â°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl 50 mM HEPES pH 7.6 2 mM EDTA 0.05% NP 40 0.5 mM DTT 0.4U/Âµl RNasin for eight times and once with 1ml ice cold 1Ã— PK buffer 100 mM Tris HCl pH 7.4 50 mM NaCl 10 mM EDTA 0.2% SDS the beads was treated i…	parent bioproject:PRJNA534030			RIP BS 0hpf	GSM3732426	source name:Zebrafish embryo\|strain:AB strain\|age:0 hpf\|tissue:whole embryo\|rip antibody:polyclonal anti Ybx1 antibody	RIP BS 0hpf	library strategy: RNA RIP BisSeq Reads were aligned to the zv9 genome assembly using meRanTK v1.2.0 m5C sites were called by meRanCall v1.2.0 and annotated by applying BEDTools’ intersectBed. MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding m5C sites in one biological replicates.	Zebrafish embryo		Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. Thus purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion then stopped by 10× RNA stop solution Ambion and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1 which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times the RNA was finally disolved in 75 μl nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer’s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 125 bp.		strain:AB strain\|age:0 hpf\|tissue:whole embryo\|rip antibody:polyclonal anti Ybx1 antibody	GSM3732426	GSM3732426: RIP BS 0hpf; Danio rerio; OTHER	GSM3732426		1	Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. Thus purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion then stopped by 10× RNA stop solution Ambion and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1 which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times the RNA was finally disolved in 75 μl nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer's instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 125 bp.	GEO Accession:GSM3732426	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP162876		RIP-BS_0hpf_R1.fastq.gz RIP-BS_0hpf_R2.fastq.gz	fastq fastq	41224496700.0	137414989.0	GSM3732426 r1	0:150 1:150	A:11515809359;C:9072060634;G:9856717145;T:10775122637;N:4786925	150	150	11515809359	9072060634	9856717145	10775122637	4786925	SRX5717519	SRS4655939	SRA786939	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.00575	0.00421	0.00122	0.00083	0.99738	0.99801	0.70652	0.78053	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	full_length	random_priming	smarter	bulk	clip	iclip	China	2019-04-22	Zygote	Embryo	Whole Organism	All anatomical structures
49541	49541	SRR8937003	SRX5717516	SRS4655936	SRP162876	PRJNA493828	Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo sample.	GSE120646	Other	The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo. RIP seq: Briefly 500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl 10 mM HEPES pH 7.6 2 mM EDTA 0.5% NP 40 0.5 mM DTT 1:100 protease inhibitor cocktail 0.4 U/Î¼l RNasin by rotating at 4Â°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4Â°C for 1 h. 50 Î¼l pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax China and 30 Î¼l Protein A Dynabeads for 4 h at 4Â°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl 50 mM HEPES pH 7.6 2 mM EDTA 0.05% NP 40 0.5 mM DTT 0.4U/Âµl RNasin for eight times and once with 1ml ice cold 1Ã— PK buffer 100 mM Tris HCl pH 7.4 50 mM NaCl 10 mM EDTA 0.2% SDS the beads was treated i…	parent bioproject:PRJNA534030			RIP INPUT 0hpf rep2	GSM3732423	source name:RIP INPUT 0hpf\|strain:AB strain\|age:0 hpf\|tissue:whole embryo	RIP INPUT 0hpf rep2	Reads were aligned to the zv9 genome assembly using TopHat v2.1.1. MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.	RIP INPUT 0hpf		Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 150 bp.		strain:AB strain\|age:0 hpf\|tissue:whole embryo	GSM3732423	GSM3732423: RIP INPUT 0hpf rep2; Danio rerio; RIP Seq	GSM3732423		1	Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 150 bp.	GEO Accession:GSM3732423	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP162876		RIP-INPUT_0hpf_rep2_R1.fastq.gz RIP-INPUT_0hpf_rep2_R2.fastq.gz	fastq fastq	17402218800.0	58007396.0	GSM3732423 r1	0:150 1:150	A:3416144403;C:5315174821;G:5345201218;T:3320906221;N:4792137	150	150	3416144403	5315174821	5345201218	3320906221	4792137	SRX5717516	SRS4655936	SRA786939	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.9819	0.9814	0.33605	0.34016	0.93458	0.93963	0.90172	0.91272	150	150	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	smarter	bulk	clip	iclip	China	2019-04-22	Zygote	Embryo	Whole Organism	All anatomical structures
49542	49542	SRR8937002	SRX5717515	SRS4655935	SRP162876	PRJNA493828	Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo sample.	GSE120646	Other	The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo. RIP seq: Briefly 500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl 10 mM HEPES pH 7.6 2 mM EDTA 0.5% NP 40 0.5 mM DTT 1:100 protease inhibitor cocktail 0.4 U/Î¼l RNasin by rotating at 4Â°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4Â°C for 1 h. 50 Î¼l pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax China and 30 Î¼l Protein A Dynabeads for 4 h at 4Â°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl 50 mM HEPES pH 7.6 2 mM EDTA 0.05% NP 40 0.5 mM DTT 0.4U/Âµl RNasin for eight times and once with 1ml ice cold 1Ã— PK buffer 100 mM Tris HCl pH 7.4 50 mM NaCl 10 mM EDTA 0.2% SDS the beads was treated i…	parent bioproject:PRJNA534030			RIP INPUT 0hpf rep1	GSM3732422	source name:RIP INPUT 0hpf\|strain:AB strain\|age:0 hpf\|tissue:whole embryo	RIP INPUT 0hpf rep1	Reads were aligned to the zv9 genome assembly using TopHat v2.1.1. MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.	RIP INPUT 0hpf		Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 150 bp.		strain:AB strain\|age:0 hpf\|tissue:whole embryo	GSM3732422	GSM3732422: RIP INPUT 0hpf rep1; Danio rerio; RIP Seq	GSM3732422		1	Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 150 bp.	GEO Accession:GSM3732422	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP162876		RIP-INPUT_0hpf_rep1_R1.fastq.gz RIP-INPUT_0hpf_rep1_R2.fastq.gz	fastq fastq	16615204800.0	55384016.0	GSM3732422 r1	0:150 1:150	A:2869477028;C:5392959051;G:5575878422;T:2776252538;N:637761	150	150	2869477028	5392959051	5575878422	2776252538	637761	SRX5717515	SRS4655935	SRA786939	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.97584	0.96561	0.04007	0.03832	0.9262	0.933	0.94642	0.94376	150	150	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	smarter	bulk	clip	iclip	China	2019-04-22	Zygote	Embryo	Whole Organism	All anatomical structures
49545	49545	SRR8936999	SRX5717512	SRS4655932	SRP162876	PRJNA493828	Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo sample.	GSE120646	Other	The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo. RIP seq: Briefly 500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl 10 mM HEPES pH 7.6 2 mM EDTA 0.5% NP 40 0.5 mM DTT 1:100 protease inhibitor cocktail 0.4 U/Î¼l RNasin by rotating at 4Â°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4Â°C for 1 h. 50 Î¼l pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax China and 30 Î¼l Protein A Dynabeads for 4 h at 4Â°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl 50 mM HEPES pH 7.6 2 mM EDTA 0.05% NP 40 0.5 mM DTT 0.4U/Âµl RNasin for eight times and once with 1ml ice cold 1Ã— PK buffer 100 mM Tris HCl pH 7.4 50 mM NaCl 10 mM EDTA 0.2% SDS the beads was treated i…	parent bioproject:PRJNA534030			RIP 0hpf rep2	GSM3732419	source name:RIP 0hpf\|strain:AB strain\|age:0 hpf\|tissue:whole embryo\|rip antibody:rabbit polyclonal anti Ybx1 antibody	RIP 0hpf rep2	Reads were aligned to the zv9 genome assembly using TopHat v2.1.1. MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.	RIP 0hpf		Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 150 bp.		strain:AB strain\|age:0 hpf\|tissue:whole embryo\|rip antibody:rabbit polyclonal anti Ybx1 antibody	GSM3732419	GSM3732419: RIP 0hpf rep2; Danio rerio; RIP Seq	GSM3732419		1	Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 150 bp.	GEO Accession:GSM3732419	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP162876		RIP_0hpf_rep2_R1.fastq.gz RIP_0hpf_rep2_R2.fastq.gz	fastq fastq	14319153300.0	47730511.0	GSM3732419 r1	0:150 1:150	A:3633266473;C:3581763715;G:3602109377;T:3500497801;N:1515934	150	150	3633266473	3581763715	3602109377	3500497801	1515934	SRX5717512	SRS4655932	SRA786939	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.96309	0.96299	0.09978	0.09922	0.80012	0.80635	0.7641	0.76535	150	150	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	smarter	bulk	clip	iclip	China	2019-04-22	Zygote	Embryo	Whole Organism	All anatomical structures
49546	49546	SRR8936998	SRX5717511	SRS4655931	SRP162876	PRJNA493828	Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo sample.	GSE120646	Other	The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo. RIP seq: Briefly 500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl 10 mM HEPES pH 7.6 2 mM EDTA 0.5% NP 40 0.5 mM DTT 1:100 protease inhibitor cocktail 0.4 U/Î¼l RNasin by rotating at 4Â°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4Â°C for 1 h. 50 Î¼l pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax China and 30 Î¼l Protein A Dynabeads for 4 h at 4Â°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl 50 mM HEPES pH 7.6 2 mM EDTA 0.05% NP 40 0.5 mM DTT 0.4U/Âµl RNasin for eight times and once with 1ml ice cold 1Ã— PK buffer 100 mM Tris HCl pH 7.4 50 mM NaCl 10 mM EDTA 0.2% SDS the beads was treated i…	parent bioproject:PRJNA534030			RIP 0hpf rep1	GSM3732418	source name:RIP 0hpf\|strain:AB strain\|age:0 hpf\|tissue:whole embryo\|rip antibody:rabbit polyclonal anti Ybx1 antibody	RIP 0hpf rep1	Reads were aligned to the zv9 genome assembly using TopHat v2.1.1. MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.	RIP 0hpf		Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 150 bp.		strain:AB strain\|age:0 hpf\|tissue:whole embryo\|rip antibody:rabbit polyclonal anti Ybx1 antibody	GSM3732418	GSM3732418: RIP 0hpf rep1; Danio rerio; RIP Seq	GSM3732418		1	Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 150 bp.	GEO Accession:GSM3732418	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP162876		RIP_0hpf_rep1_R1.fastq.gz RIP_0hpf_rep1_R2.fastq.gz	fastq fastq	7807878000.0	26026260.0	GSM3732418 r1	0:150 1:150	A:1698013251;C:2200605244;G:2305251364;T:1602824248;N:1183893	150	150	1698013251	2200605244	2305251364	1602824248	1183893	SRX5717511	SRS4655931	SRA786939	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.89154	0.89105	0.26373	0.26886	0.82477	0.827	0.79125	0.77711	150	150	B	B	biological fallback assumption	illumina	hiseq_era	full_length	random_priming	smarter	bulk	clip	iclip	China	2019-04-22	Zygote	Embryo	Whole Organism	All anatomical structures
49563	49563	SRR7942622	SRX4776887	SRS3857428	SRP162875	PRJNA493829	m5C profiles in zebrafish embryo sample.	GSE120645	Other	Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion then stopped by 10× RNA stop solution Ambion and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1 which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times the RNA was finally disolved in 75 µl nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer's instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 125 bp. Overall design: Examination of m5C levels in zebrafish embryo.				WT 0hpf m5C rep2	GSM3406888	source name:Zebrafish embryo\|strain:AB strain\|cell type:Zebrafish embryo\|age:0 hpf\|tissue:whole embryo	WT 0hpf m5C rep2	Reads were aligned to the zv9 and hg19 genome assembly using meRanTK v1.2.0 m5C sites were called by meRanCall v1.2.0 and annotated by applying BEDTools’ intersectBed. Genome build: zv9 and hg19 Supplementary files format and content: m5C sites in two biological replicates.	Zebrafish embryo		Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. Thus purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion then stopped by 10× RNA stop solution Ambion and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1 which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times the RNA was finally disolved in 75 μl nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer’s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 125 bp. RNA BisSeq		strain:AB strain\|cell type:Zebrafish embryo\|age:0 hpf\|tissue:whole embryo	GSM3406888	GSM3406888: WT 0hpf m5C rep2; Danio rerio; OTHER	GSM3406888		1	Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. Thus purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion then stopped by 10× RNA stop solution Ambion and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1 which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times the RNA was finally disolved in 75 μl nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer's instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 125 bp. RNA BisSeq	GEO Accession:GSM3406888	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP162875		WT_0hpf_rep2_m5C_R1.fastq.gz WT_0hpf_rep2_m5C_R2.fastq.gz	fastq fastq	21201784250.0	84807137.0	GSM3406888 r1	0:125 1:125	A:7176675495;C:3469343240;G:3951404122;T:6579575790;N:24785603	125	125	7176675495	3469343240	3951404122	6579575790	24785603	SRX4776887	SRS3857428	SRA786937	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.00074	0.00077	0.00015	0.00015	0.99835	0.99829	0.62037	0.64035	125	125	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2018-09-28	Zygote	Embryo	Whole Organism	All anatomical structures
49564	49564	SRR7942621	SRX4776886	SRS3857426	SRP162875	PRJNA493829	m5C profiles in zebrafish embryo sample.	GSE120645	Other	Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion then stopped by 10× RNA stop solution Ambion and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1 which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times the RNA was finally disolved in 75 µl nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer's instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 125 bp. Overall design: Examination of m5C levels in zebrafish embryo.				WT 0hpf m5C rep1	GSM3406887	source name:Zebrafish embryo\|strain:AB strain\|cell type:Zebrafish embryo\|age:0 hpf\|tissue:whole embryo	WT 0hpf m5C rep1	Reads were aligned to the zv9 and hg19 genome assembly using meRanTK v1.2.0 m5C sites were called by meRanCall v1.2.0 and annotated by applying BEDTools’ intersectBed. Genome build: zv9 and hg19 Supplementary files format and content: m5C sites in two biological replicates.	Zebrafish embryo		Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. Thus purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion then stopped by 10× RNA stop solution Ambion and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1 which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times the RNA was finally disolved in 75 μl nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer’s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 125 bp. RNA BisSeq		strain:AB strain\|cell type:Zebrafish embryo\|age:0 hpf\|tissue:whole embryo	GSM3406887	GSM3406887: WT 0hpf m5C rep1; Danio rerio; OTHER	GSM3406887		1	Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. Thus purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion then stopped by 10× RNA stop solution Ambion and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1 which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times the RNA was finally disolved in 75 μl nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer's instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode creating reads with a length of 125 bp. RNA BisSeq	GEO Accession:GSM3406887	OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP162875		WT_0hpf_rep1_m5C_R1.fastq.gz WT_0hpf_rep1_m5C_R2.fastq.gz	fastq fastq	25405235500.0	101620942.0	GSM3406887 r1	0:125 1:125	A:8768618269;C:3912734696;G:4276708166;T:8422886588;N:24287781	125	125	8768618269	3912734696	4276708166	8422886588	24287781	SRX4776886	SRS3857426	SRA786937	GEO	Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)	2	0.0011	0.00103	0.00022	0.00018	0.9977	0.99786	0.60493	0.60256	125	125	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2018-09-28	Zygote	Embryo	Whole Organism	All anatomical structures
55275	55275	SRR10215491	SRX6935164	SRS5465199	SRP223930	PRJNA575342	CAGE /CappedRNA sequencig	PRJNA575342	Other	CAGE and full length capped RNA sequencing for identification of transcription start TSS utilisation during Zebrafish Danio rerio embryonic development					S01 1Cell	strain:AB\|dev stage:1cell\|sex:N/A\|tissue:whole embryo\|BioSampleModel:Model organism or animal									CAGE seq of Danio rerio whole embryo 1 cell stage	1Cell nAnTiCAGE	1Cell nAnTiCAGE	nAnTiCAGE			RNA-Seq	TRANSCRIPTOMIC	CAGE	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP223930		S01_1Cells_nAnTiCAGE_1.fastq.gz S01_1Cells_nAnTiCAGE_2.fastq.gz	fastq fastq	1193891117.0	6060361.0	S01 1Cells nAnTiCAGE 1.fastq.gz	0:97 1:100	A:286037352;C:298140071;G:310668851;T:297430066;N:1614777	97	100	286037352	298140071	310668851	297430066	1614777	SRX6935164	SRS5465199	SRA971223	University of Birmingham\|Cancer and Genomic Sciences	University of Birmingham	2	0.93733	0.97059	0.08219	0.07881	0.76682	0.75834	0.53879	0.54537	97	100	B	B	biological fallback assumption	illumina	hiseq_era	full_length	cage	unknown	bulk	unknown	unknown	United Kingdom	2019-10-02	Zygote	Embryo	Whole Organism	All anatomical structures
55860	55860	SRR10863001	SRX7533067	SRS5972255	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.			The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.		wt zygote 0hpf rep3	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:0hpf\|dev stage:zygote\|sex:not applicable\|tissue:whole embryo\|biological replicate:replicate 3\|BioSampleModel:Model organism or animal									totalRNA of Zebrafish: zygote 0hpf	wt zygote 0hpf rep3 totalRNA	wt zygote 0hpf rep3 totalRNA	NGS library prep was performed with NuGen Ovation SoLo RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 14 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2.0 Fluorometer Life technologies. Samples were pooled in equimolar ratio and sequenced PE for 2x 75 cycles plus 16 cycles for the index read. Small RNA sequencing			RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	NextSeq 550	SRP241074		09072018-wt_zygote_0hpf_rep3_totalRNA.R1.fastq.gz 09072018-wt_zygote_0hpf_rep3_totalRNA.R2.fastq.gz 30052018-wt_zygote_0hpf_rep3_totalRNA.R1.fastq.gz 30052018-wt_zygote_0hpf_rep3_totalRNA.R2.fastq.gz	fastq fastq fastq fastq	4458621474.0	30620736.0	09072018 wt zygote 0hpf rep3 totalRNA.R1.fastq.gz	0:72.80 1:72.80	A:1208331512;C:1036387532;G:1015612570;T:1198148120;N:141740	72	72	1208331512	1036387532	1015612570	1198148120	141740	SRX7533067	SRS5972255	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.95239	0.95309	0.06336	0.06309	0.77703	0.77901	0.70327	0.70174	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	bulk	unknown	unknown	Germany	2020-01-10	Zygote	Embryo	Whole Organism	All anatomical structures
55861	55861	SRR10863002	SRX7533066	SRS5972254	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.			The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.		wt zygote 0hpf rep2	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:0hpf\|dev stage:zygote\|sex:not applicable\|tissue:whole embryo\|biological replicate:replicate 2\|BioSampleModel:Model organism or animal									totalRNA of Zebrafish: zygote 0hpf	wt zygote 0hpf rep2 totalRNA	wt zygote 0hpf rep2 totalRNA	NGS library prep was performed with NuGen Ovation SoLo RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 14 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2.0 Fluorometer Life technologies. Samples were pooled in equimolar ratio and sequenced PE for 2x 75 cycles plus 16 cycles for the index read. Small RNA sequencing			RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	NextSeq 550	SRP241074		30052018-wt_zygote_0hpf_rep2_totalRNA.R2.fastq.gz 30052018-wt_zygote_0hpf_rep2_totalRNA.R1.fastq.gz 09072018-wt_zygote_0hpf_rep2_totalRNA.R2.fastq.gz 09072018-wt_zygote_0hpf_rep2_totalRNA.R1.fastq.gz	fastq fastq fastq fastq	4071628788.0	27966671.0	09072018 wt zygote 0hpf rep2 totalRNA.R1.fastq.gz	0:72.79 1:72.79	A:1109401096;C:941703799;G:920259964;T:1100136253;N:127676	72	72	1109401096	941703799	920259964	1100136253	127676	SRX7533066	SRS5972254	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.95344	0.95216	0.06464	0.064	0.77835	0.78086	0.70871	0.71004	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	bulk	unknown	unknown	Germany	2020-01-10	Zygote	Embryo	Whole Organism	All anatomical structures
55863	55863	SRR10863005	SRX7533064	SRS5972253	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.			The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.		wt zygote 0hpf rep1	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:0hpf\|dev stage:zygote\|sex:not applicable\|tissue:whole embryo\|biological replicate:replicate 1\|BioSampleModel:Model organism or animal									totalRNA of Zebrafish: zygote 0hpf	wt zygote 0hpf rep1 totalRNA	wt zygote 0hpf rep1 totalRNA	NGS library prep was performed with NuGen Ovation SoLo RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 14 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2.0 Fluorometer Life technologies. Samples were pooled in equimolar ratio and sequenced PE for 2x 75 cycles plus 16 cycles for the index read. Small RNA sequencing			RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	NextSeq 550	SRP241074		09072018-wt_zygote_0hpf_rep1_totalRNA.R1.fastq.gz 09072018-wt_zygote_0hpf_rep1_totalRNA.R2.fastq.gz 30052018-wt_zygote_0hpf_rep1_totalRNA.R1.fastq.gz 30052018-wt_zygote_0hpf_rep1_totalRNA.R2.fastq.gz	fastq fastq fastq fastq	4015382154.0	27584968.0	09072018 wt zygote 0hpf rep1 totalRNA.R1.fastq.gz	0:72.78 1:72.78	A:1092464298;C:930179967;G:907966263;T:1084644388;N:127238	72	72	1092464298	930179967	907966263	1084644388	127238	SRX7533064	SRS5972253	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.95247	0.95275	0.06393	0.0634	0.7782	0.7805	0.70719	0.70435	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	random_priming	unknown	bulk	unknown	unknown	Germany	2020-01-10	Zygote	Embryo	Whole Organism	All anatomical structures
55883	55883	SRR10863025	SRX7533044	SRS5972254	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.			The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.		wt zygote 0hpf rep2	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:0hpf\|dev stage:zygote\|sex:not applicable\|tissue:whole embryo\|biological replicate:replicate 2\|BioSampleModel:Model organism or animal									small RNA of Zebrafish: zygotes 0hpf	imb ketting 2018 19 redl smRNA 07 0hpf zygotes rep2 S30.R1	imb ketting 2018 19 redl smRNA 07 0hpf zygotes rep2 S30.R1	Next Flex small RNA seq kit v3 from BIOO scientific starting from 1ng of total RNA. Followed the protocol version V16.06 diluting the adaptors for ligation and using 25 PCR cycles for library amplification. The library was size selected using an 8% TBE gel and the library fragments of 146 168bp corresponding to insert sizes of 18 40bp were recovered and purified.			ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 550	SRP241074		imb_ketting_2018_19_redl_smRNA-07_0hpf_zygotes_rep2_S30.R1.fastq.gz	fastq	1083028275.0	14440377.0	imb ketting 2018 19 redl smRNA 07 0hpf zygotes rep2 S30.R1.fastq.gz	0:75 1:0	A:261596209;C:277009311;G:258733780;T:285678456;N:10519	75	0	261596209	277009311	258733780	285678456	10519	SRX7533044	SRS5972254	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	1	0.00065		8e-05		0.99906		0.73076		75		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Germany	2020-01-10	Zygote	Embryo	Whole Organism	All anatomical structures
55884	55884	SRR10863026	SRX7533043	SRS5972253	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.			The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.		wt zygote 0hpf rep1	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:0hpf\|dev stage:zygote\|sex:not applicable\|tissue:whole embryo\|biological replicate:replicate 1\|BioSampleModel:Model organism or animal									small RNA of Zebrafish: zygotes 0hpf	imb ketting 2018 19 redl smRNA 06 0hpf zygotes rep1 S29.R1	imb ketting 2018 19 redl smRNA 06 0hpf zygotes rep1 S29.R1	Next Flex small RNA seq kit v3 from BIOO scientific starting from 1ng of total RNA. Followed the protocol version V16.06 diluting the adaptors for ligation and using 25 PCR cycles for library amplification. The library was size selected using an 8% TBE gel and the library fragments of 146 168bp corresponding to insert sizes of 18 40bp were recovered and purified.			ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 550	SRP241074		imb_ketting_2018_19_redl_smRNA-06_0hpf_zygotes_rep1_S29.R1.fastq.gz	fastq	1094583075.0	14594441.0	imb ketting 2018 19 redl smRNA 06 0hpf zygotes rep1 S29.R1.fastq.gz	0:75 1:0	A:272231426;C:272258006;G:282795391;T:267287656;N:10596	75	0	272231426	272258006	282795391	267287656	10596	SRX7533043	SRS5972253	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	1	0.00035		7e-05		0.99935		0.63043		75		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Germany	2020-01-10	Zygote	Embryo	Whole Organism	All anatomical structures
55897	55897	SRR10863038	SRX7533030	SRS5972255	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.			The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.		wt zygote 0hpf rep3	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:0hpf\|dev stage:zygote\|sex:not applicable\|tissue:whole embryo\|biological replicate:replicate 3\|BioSampleModel:Model organism or animal									mRNA of Zebrafish: zygotes 0hpf	imb ketting 2018 18 redl SmartSeq2 08 0hpf zygotes rep3 S25	imb ketting 2018 18 redl SmartSeq2 08 0hpf zygotes rep3 S25	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074		imb_ketting_2018_18_redl_SmartSeq2-08_0hpf_zygotes_rep3_S25.R1.fastq.gz imb_ketting_2018_18_redl_SmartSeq2-08_0hpf_zygotes_rep3_S25.R2.fastq.gz	fastq fastq	2254742850.0	15031619.0	imb ketting 2018 18 redl SmartSeq2 08 0hpf zygotes rep3 S25.R1.fastq.gz	0:75 1:75	A:601169757;C:521134633;G:522514682;T:609902670;N:21108	75	75	601169757	521134633	522514682	609902670	21108	SRX7533030	SRS5972255	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.94461	0.94575	0.01803	0.01807	0.76751	0.76883	0.49585	0.49808	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Zygote	Embryo	Whole Organism	All anatomical structures
55898	55898	SRR10863039	SRX7533029	SRS5972255	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.			The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.		wt zygote 0hpf rep3	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:0hpf\|dev stage:zygote\|sex:not applicable\|tissue:whole embryo\|biological replicate:replicate 3\|BioSampleModel:Model organism or animal									small RNA of Zebrafish: zygotes 0hpf	imb ketting 2018 19 redl smRNA 08 0hpf zygotes rep3 S31.R1	imb ketting 2018 19 redl smRNA 08 0hpf zygotes rep3 S31.R1	Next Flex small RNA seq kit v3 from BIOO scientific starting from 1ng of total RNA. Followed the protocol version V16.06 diluting the adaptors for ligation and using 25 PCR cycles for library amplification. The library was size selected using an 8% TBE gel and the library fragments of 146 168bp corresponding to insert sizes of 18 40bp were recovered and purified.			ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	NextSeq 550	SRP241074		imb_ketting_2018_19_redl_smRNA-08_0hpf_zygotes_rep3_S31.R1.fastq.gz	fastq	1174146225.0	15655283.0	imb ketting 2018 19 redl smRNA 08 0hpf zygotes rep3 S31.R1.fastq.gz	0:75 1:0	A:275690402;C:320014688;G:295706949;T:282722725;N:11461	75	0	275690402	320014688	295706949	282722725	11461	SRX7533029	SRS5972255	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	1	0.00017		2e-05		0.99977		0.26315		75		T		under 1.2% mapping rate	illumina	nextseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	Germany	2020-01-10	Zygote	Embryo	Whole Organism	All anatomical structures
55899	55899	SRR10863040	SRX7533028	SRS5972254	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.			The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.		wt zygote 0hpf rep2	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:0hpf\|dev stage:zygote\|sex:not applicable\|tissue:whole embryo\|biological replicate:replicate 2\|BioSampleModel:Model organism or animal									mRNA of Zebrafish: zygotes 0hpf	imb ketting 2018 18 redl SmartSeq2 07 0hpf zygotes rep2 S24	imb ketting 2018 18 redl SmartSeq2 07 0hpf zygotes rep2 S24	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074		imb_ketting_2018_18_redl_SmartSeq2-07_0hpf_zygotes_rep2_S24.R1.fastq.gz imb_ketting_2018_18_redl_SmartSeq2-07_0hpf_zygotes_rep2_S24.R2.fastq.gz	fastq fastq	2415051600.0	16100344.0	imb ketting 2018 18 redl SmartSeq2 07 0hpf zygotes rep2 S24.R1.fastq.gz	0:75 1:75	A:644001016;C:558385744;G:560491907;T:652150600;N:22333	75	75	644001016	558385744	560491907	652150600	22333	SRX7533028	SRS5972254	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.9462	0.94755	0.02097	0.02075	0.76694	0.76909	0.4948	0.49938	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Zygote	Embryo	Whole Organism	All anatomical structures
55900	55900	SRR10863041	SRX7533027	SRS5972253	SRP241074	PRJNA597223	Danio rerio primordial germ cell expression pofiling	PRJNA597223	Whole Genome Sequencing	Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.			The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.		wt zygote 0hpf rep1	strain:vasa:eGFP\|isolate:not applicable\|breed:TUE\|cultivar:not applicable\|ecotype:not applicable\|age:0hpf\|dev stage:zygote\|sex:not applicable\|tissue:whole embryo\|biological replicate:replicate 1\|BioSampleModel:Model organism or animal									mRNA of Zebrafish: zygotes 0hpf	imb ketting 2018 18 redl SmartSeq2 06 0hpf zygotes rep1 S23	imb ketting 2018 18 redl SmartSeq2 06 0hpf zygotes rep1 S23	Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 550	SRP241074		imb_ketting_2018_18_redl_SmartSeq2-06_0hpf_zygotes_rep1_S23.R1.fastq.gz imb_ketting_2018_18_redl_SmartSeq2-06_0hpf_zygotes_rep1_S23.R2.fastq.gz	fastq fastq	2621759100.0	17478394.0	imb ketting 2018 18 redl SmartSeq2 06 0hpf zygotes rep1 S23.R1.fastq.gz	0:75 1:75	A:697302326;C:607756156;G:612217195;T:704460378;N:23045	75	75	697302326	607756156	612217195	704460378	23045	SRX7533027	SRS5972253	SRA1023320	Rene Ketting group\|Ketting Lab	Rene Ketting group	2	0.94882	0.95052	0.02124	0.02139	0.77082	0.7724	0.49237	0.49259	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_plate	smartseq	Germany	2020-01-10	Zygote	Embryo	Whole Organism	All anatomical structures
61762	61762	SRR13015620	SRX9466616	SRS7678764	SRP291905	PRJNA674002	A to I RNA editing in zebrafish during development	PRJNA674002	Other	Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.				zebrafish embryos 0 hpf	single cross 2 0hpf.rep2	strain:AB wildtype\|dev stage:0 hpf\|sex:unknown\|tissue:whole embryo\|embryos derived by cross:single cross 2\|biological replicate:replicate 2\|assay type:mRNA seq\|BioSampleModel:Model organism or animal									mRNA seq of whole zebrafish embryos wildtype AB 0 hpf single cross 2 Rep2 lane2	PJ KH 004 2	PJ KH 004 2	stranded mRNA			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP291905		PJ_KH_004_S4_L002_R1_001.fastq.gz PJ_KH_004_S4_L002_R2_001.fastq.gz	fastq fastq	6747035756.0	22341178.0	PJ KH 004 S4 L002 R1 001.fastq.gz	0:151 1:151	A:1749259364;C:1630082050;G:1671975335;T:1694420838;N:1298169	151	151	1749259364	1630082050	1671975335	1694420838	1298169	SRX9466616	SRS7678764	SRA1153075	MDC Berlin\|BIMSB	MDC Berlin	2	0.91606	0.915	0.0228	0.02253	0.8462	0.84764	0.47581	0.47811	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Germany	2020-11-10	Zygote	Embryo	Whole Organism	All anatomical structures
61763	61763	SRR13015621	SRX9466615	SRS7678764	SRP291905	PRJNA674002	A to I RNA editing in zebrafish during development	PRJNA674002	Other	Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.				zebrafish embryos 0 hpf	single cross 2 0hpf.rep2	strain:AB wildtype\|dev stage:0 hpf\|sex:unknown\|tissue:whole embryo\|embryos derived by cross:single cross 2\|biological replicate:replicate 2\|assay type:mRNA seq\|BioSampleModel:Model organism or animal									mRNA seq of whole zebrafish embryos wildtype AB 0 hpf single cross 2 Rep2 lane1	PJ KH 004 1	PJ KH 004 1	stranded mRNA			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP291905		PJ_KH_004_S4_L001_R1_001.fastq.gz PJ_KH_004_S4_L001_R2_001.fastq.gz	fastq fastq	7002326926.0	23186513.0	PJ KH 004 S4 L001 R1 001.fastq.gz	0:151 1:151	A:1813808137;C:1692625163;G:1737142909;T:1756973437;N:1777280	151	151	1813808137	1692625163	1737142909	1756973437	1777280	SRX9466615	SRS7678764	SRA1153075	MDC Berlin\|BIMSB	MDC Berlin	2	0.91797	0.91431	0.02335	0.02297	0.84682	0.84867	0.48058	0.47562	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Germany	2020-11-10	Zygote	Embryo	Whole Organism	All anatomical structures
61764	61764	SRR13015622	SRX9466614	SRS7678763	SRP291905	PRJNA674002	A to I RNA editing in zebrafish during development	PRJNA674002	Other	Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.				zebrafish embryos 0 hpf	single cross 2 0hpf.rep1	strain:AB wildtype\|dev stage:0 hpf\|sex:unknown\|tissue:whole embryo\|embryos derived by cross:single cross 2\|biological replicate:replicate 1\|assay type:mRNA seq\|BioSampleModel:Model organism or animal									mRNA seq of whole zebrafish embryos wildtype AB 0 hpf single cross 2 Rep1 lane2	PJ KH 003 2	PJ KH 003 2	stranded mRNA			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP291905		PJ_KH_003_S3_L002_R1_001.fastq.gz PJ_KH_003_S3_L002_R2_001.fastq.gz	fastq fastq	6323928622.0	20940161.0	PJ KH 003 S3 L002 R1 001.fastq.gz	0:151 1:151	A:1664173214;C:1500258415;G:1538972894;T:1619319465;N:1204634	151	151	1664173214	1500258415	1538972894	1619319465	1204634	SRX9466614	SRS7678763	SRA1153075	MDC Berlin\|BIMSB	MDC Berlin	2	0.91771	0.91711	0.02141	0.02071	0.84382	0.84632	0.4721	0.47896	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Germany	2020-11-10	Zygote	Embryo	Whole Organism	All anatomical structures
61766	61766	SRR13015624	SRX9466612	SRS7678763	SRP291905	PRJNA674002	A to I RNA editing in zebrafish during development	PRJNA674002	Other	Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.				zebrafish embryos 0 hpf	single cross 2 0hpf.rep1	strain:AB wildtype\|dev stage:0 hpf\|sex:unknown\|tissue:whole embryo\|embryos derived by cross:single cross 2\|biological replicate:replicate 1\|assay type:mRNA seq\|BioSampleModel:Model organism or animal									mRNA seq of whole zebrafish embryos wildtype AB 0 hpf single cross 2 Rep1 lane1	PJ KH 003 1	PJ KH 003 1	stranded mRNA			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP291905		PJ_KH_003_S3_L001_R1_001.fastq.gz PJ_KH_003_S3_L001_R2_001.fastq.gz	fastq fastq	6652658038.0	22028669.0	PJ KH 003 S3 L001 R1 001.fastq.gz	0:151 1:151	A:1748718497;C:1579368495;G:1621147905;T:1701739850;N:1683291	151	151	1748718497	1579368495	1621147905	1701739850	1683291	SRX9466612	SRS7678763	SRA1153075	MDC Berlin\|BIMSB	MDC Berlin	2	0.91835	0.91483	0.02199	0.02155	0.84262	0.84471	0.4828	0.4803	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Germany	2020-11-10	Zygote	Embryo	Whole Organism	All anatomical structures
61767	61767	SRR13015625	SRX9466611	SRS7678761	SRP291905	PRJNA674002	A to I RNA editing in zebrafish during development	PRJNA674002	Other	Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.				zebrafish embryos 0 hpf	single cross 1 0hpf.rep2	strain:AB wildtype\|dev stage:0 hpf\|sex:unknown\|tissue:whole embryo\|embryos derived by cross:single cross 1\|biological replicate:replicate 2\|assay type:mRNA seq\|BioSampleModel:Model organism or animal									mRNA seq of whole zebrafish embryos wildtype AB 0 hpf single cross 1 Rep2 lane2	PJ KH 002 2	PJ KH 002 2	stranded mRNA			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP291905		PJ_KH_002_S2_L002_R1_001.fastq.gz PJ_KH_002_S2_L002_R2_001.fastq.gz	fastq fastq	7116731170.0	23565335.0	PJ KH 002 S2 L002 R1 001.fastq.gz	0:151 1:151	A:1813322250;C:1745818869;G:1791244865;T:1764990020;N:1355166	151	151	1813322250	1745818869	1791244865	1764990020	1355166	SRX9466611	SRS7678761	SRA1153075	MDC Berlin\|BIMSB	MDC Berlin	2	0.90942	0.90881	0.01338	0.01286	0.83512	0.8365	0.47569	0.47472	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Germany	2020-11-10	Zygote	Embryo	Whole Organism	All anatomical structures
61768	61768	SRR13015626	SRX9466610	SRS7678761	SRP291905	PRJNA674002	A to I RNA editing in zebrafish during development	PRJNA674002	Other	Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.				zebrafish embryos 0 hpf	single cross 1 0hpf.rep2	strain:AB wildtype\|dev stage:0 hpf\|sex:unknown\|tissue:whole embryo\|embryos derived by cross:single cross 1\|biological replicate:replicate 2\|assay type:mRNA seq\|BioSampleModel:Model organism or animal									mRNA seq of whole zebrafish embryos wildtype AB 0 hpf single cross 1 Rep2 lane1	PJ KH 002 1	PJ KH 002 1	stranded mRNA			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP291905		PJ_KH_002_S2_L001_R1_001.fastq.gz PJ_KH_002_S2_L001_R2_001.fastq.gz	fastq fastq	7285422632.0	24123916.0	PJ KH 002 S2 L001 R1 001.fastq.gz	0:151 1:151	A:1854975023;C:1787715446;G:1835538323;T:1805336454;N:1857386	151	151	1854975023	1787715446	1835538323	1805336454	1857386	SRX9466610	SRS7678761	SRA1153075	MDC Berlin\|BIMSB	MDC Berlin	2	0.90695	0.90384	0.01372	0.01325	0.83644	0.83806	0.48376	0.46874	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Germany	2020-11-10	Zygote	Embryo	Whole Organism	All anatomical structures
61769	61769	SRR13015627	SRX9466609	SRS7678760	SRP291905	PRJNA674002	A to I RNA editing in zebrafish during development	PRJNA674002	Other	Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.				zebrafish embryos 0 hpf	single cross 1 0hpf.rep1	strain:AB wildtype\|dev stage:0 hpf\|sex:unknown\|tissue:whole embryo\|embryos derived by cross:single cross 1\|biological replicate:replicate 1\|assay type:mRNA seq\|BioSampleModel:Model organism or animal									mRNA seq of whole zebrafish embryos wildtype AB 0 hpf single cross 1 Rep1 lane2	PJ KH 001 2	PJ KH 001 2	stranded mRNA			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP291905		PJ_KH_001_S1_L002_R1_001.fastq.gz PJ_KH_001_S1_L002_R2_001.fastq.gz	fastq fastq	5744360120.0	19021060.0	PJ KH 001 S1 L002 R1 001.fastq.gz	0:151 1:151	A:1471481677;C:1411353282;G:1443418761;T:1417001880;N:1104520	151	151	1471481677	1411353282	1443418761	1417001880	1104520	SRX9466609	SRS7678760	SRA1153075	MDC Berlin\|BIMSB	MDC Berlin	2	0.78051	0.78166	0.02032	0.0196	0.84378	0.84563	0.51089	0.51533	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Germany	2020-11-10	Zygote	Embryo	Whole Organism	All anatomical structures
61770	61770	SRR13015628	SRX9466608	SRS7678760	SRP291905	PRJNA674002	A to I RNA editing in zebrafish during development	PRJNA674002	Other	Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.				zebrafish embryos 0 hpf	single cross 1 0hpf.rep1	strain:AB wildtype\|dev stage:0 hpf\|sex:unknown\|tissue:whole embryo\|embryos derived by cross:single cross 1\|biological replicate:replicate 1\|assay type:mRNA seq\|BioSampleModel:Model organism or animal									mRNA seq of whole zebrafish embryos wildtype AB 0 hpf single cross 1 Rep1 lane1	PJ KH 001 1	PJ KH 001 1	stranded mRNA			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP291905		PJ_KH_001_S1_L001_R1_001.fastq.gz PJ_KH_001_S1_L001_R2_001.fastq.gz	fastq fastq	6028405314.0	19961607.0	PJ KH 001 S1 L001 R1 001.fastq.gz	0:151 1:151	A:1542966381;C:1481961666;G:1516533761;T:1485424027;N:1519479	151	151	1542966381	1481961666	1516533761	1485424027	1519479	SRX9466608	SRS7678760	SRA1153075	MDC Berlin\|BIMSB	MDC Berlin	2	0.78061	0.77898	0.02018	0.01968	0.84508	0.84654	0.52141	0.51846	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Germany	2020-11-10	Zygote	Embryo	Whole Organism	All anatomical structures
65567	65567	SRR15373448	SRX11676000	SRS9707982	SRP331635	PRJNA753019	five prime half of specific tRNAs feeds back to promote corresponding tRNA gene transcription in vertebrate embryos [tRNA seq]	GSE181683	Transcriptome Analysis	five primetRFls are small tRNA fragments derived from five prime half of mature tRNAs. However it is unknown whether five primetRFls could feed back to regulate tRNA biogenesis. Here we show that five primetRFlGly/GCC and five primetRFlGlu/CTC function to promote transcription of corresponding tRNA genes and are essential for vertebrate early embryogenesis. During zebrafish embryogenesis dynamics of five primetRFlGly/GCC and five primetRFlGlu/CTC levels correlates with that of tRNAGly/GCC and tRNAGlu/CTC levels. Morpholino mediated knockdown of five primetRFlGly/GCC or five primetRFlGlu/CTC down regulates tRNAGly/GCC or tRNAGlu/CTC levels respectively and causes embryonic lethality that is efficiently rescued by co injection of properly refolded corresponding tRNA. In zebrafish embryos tRNA:DNA and five primetRFl:DNA hybrids commonly exist on the template strand of tRNA genes. Mechanistically unstable five primetRFl:DNA hybrid may prevent the formation of transcriptionally inhibitory stable tRNA:DNA hybrids on the same tRNA loci so as to facilitate tRNA genes transcription. The uncovered mechanism may be implicated in other physiological and pathological processes. Overall design: tRNAs from wildtype zebrafish eggs and early embryos were detected by high throughput sequencing. Total RNAs from mature egg 1cell 256c sphere shield and 24hpf stage embryos were extracted by Trizol reagent. Then 60 120 nt length RNA was enriched by separation and elution from denature gel. RNA was treated with a combination of ALKB protein to remove some modifications before library preparation.	parent bioproject:PRJNA753013	pubmed:34797706		tRNA 1cell	GSM5509227	tissue:Whole Embryo\|genotype:WT\|strain:TU\|developmental stage:1cell	tRNA 1cell	Adaptor trimming and quality control were done by FastP Version 0.19.5 and Cutadapt Version 3.4 then 60 100 nt length reads were preserved for down stream analysis. Reads were first mapped to genome GRCz11 by Bowtie2 Version 2.4.2 with very sensitive local mode D 20 R 3 N 0 L 20 i S 1 0.50. Then aligned reads were further mapped to tRNA database GtRNAdb GRCz11. The counts of reads aligned to each tRNAs were calculated and normalized to all reads mapped to genome for down stream analysis. Genome build: GRCz11 Genome build: tRNA database from GtRNAdb GRCz11 Supplementary files format and content: tab delimited text files include tRNA RPM values for each sample	Whole Embryo		About 50 100 zebrafish eggs or embryos at a desired stage were collected to extract total RNA and dechorionated by Pronase digestion. Embryos were then transferred to 1.5 ml eppendorf tube and lysed in 1 ml Trizol Reagent Thermo Fisher Scientific 15596018. The lysate was centrifuged at 12 000 rpm for 10 min and the supernatant was collected and mixed with 200 μl chloroform in a fresh tube. post centrifugation at 12 000 rpm for 10 min at 4℃ the supernatant was transferred to a fresh tube with addition of equal volume of isopropanol and incubated at room temperature for 15 min followed by thorough mix and centrifugation at 12 000 rpm for 10 20 min. The RNA pellet was washed by 75% ethanol once and was stored as pellet in 75% ethanol at 80℃ until all samples were collected. Total RNA was placed on ice for 30 min with 10% PEG8000 and 0.5 M NaCl then centrifuged at 14 000 rpm for 15 min at 4℃. Supernatant low molecular weight LMW RNA was collected and precipitated by addition of ethanol. The LMW RNA was separated by 8% 8 M Urea PAGE gel then the bands correspond to 60 120 nt length were cut and crunched into small pieces. RNA was eluted from the gel by 0.3 M NaOAc overnight on a vertical rotator at 4℃. Then the supernatant was precipitated at 20℃ post addition with 2 μl of Glycoblue and 2.5 volume of ethanol. post centrifuged at 12 000 rpm for 30 min and washed by 75% ethanol the RNA precipitant was dissolved in RNase free water. There are three pretreatment steps before library preparation. 60 120nt RNA enriched in the previous step was first incubated in 100 mM Tris HCl pH 9.0 at 37℃ for 30 min to be deacylated then the RNA was treated with T4 PNK to repair ends at 37℃ for 30 min. Modifications on tRNAs were removed by ALKB treatment [1 μg purified RNA was treated by ALKB protein mixture wt ALKB 160 pmol; ALKB D135S 200 pmol; and ALKB D135S/L118V 200 pmol in reaction buffer 300 mM KCl 2 mM MgCl2 50 μM NH42FeSO42 300 μM α ketoglutarate 2 mM vitamin C 50 μg/ml BSA 50 mM MES pH 5.0 40 U RNase I…		genotype:WT\|strain:TU\|developmental stage:1cell	GSM5509227	GSM5509227: tRNA 1cell; Danio rerio; RNA Seq	GSM5509227		1	About 50 100 zebrafish eggs or embryos at a desired stage were collected to extract total RNA and dechorionated by Pronase digestion. Embryos were then transferred to 1.5 ml eppendorf tube and lysed in 1 ml Trizol Reagent Thermo Fisher Scientific 15596018. The lysate was centrifuged at 12 000 rpm for 10 min and the supernatant was collected and mixed with 200 μl chloroform in a fresh tube. post centrifugation at 12 000 rpm for 10 min at 4℃ the supernatant was transferred to a fresh tube with addition of equal volume of isopropanol and incubated at room temperature for 15 min followed by thorough mix and centrifugation at 12 000 rpm for 10 20 min. The RNA pellet was washed by 75% ethanol once and was stored as pellet in 75% ethanol at 80℃ until all samples were collected. Total RNA was placed on ice for 30 min with 10% PEG8000 and 0.5 M NaCl then centrifuged at 14 000 rpm for 15 min at 4℃. Supernatant low molecular weight LMW RNA was collected and precipitated by addition of ethanol. The LMW RNA was separated by 8% 8 M Urea PAGE gel then the bands correspond to 60 120 nt length were cut and crunched into small pieces. RNA was eluted from the gel by 0.3 M NaOAc overnight on a vertical rotator at 4℃. Then the supernatant was precipitated at 20℃ post addition with 2 μl of Glycoblue and 2.5 volume of ethanol. post centrifuged at 12 000 rpm for 30 min and washed by 75% ethanol the RNA precipitant was dissolved in RNase free water. There are three pretreatment steps before library preparation. 60 120nt RNA enriched in the previous step was first incubated in 100 mM Tris HCl pH 9.0 at 37℃ for 30 min to be deacylated then the RNA was treated with T4 PNK to repair ends at 37℃ for 30 min. Modifications on tRNAs were removed by ALKB treatment [1 μg purified RNA was treated by ALKB protein mixture wt ALKB 160 pmol; ALKB D135S 200 pmol; and ALKB D135S/L118V 200 pmol in reaction buffer 300 mM KCl 2 mM MgCl2 50 μM NH42FeSO42 300 μM α ketoglutarate 2 mM vitamin C 50 μg/ml BSA 50 mM MES pH 5.0 40 U RNase I…	GEO Accession:GSM5509227	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP331635		tRNA_1cell_1.fq.gz tRNA_1cell_2.fq.gz	fastq fastq	9361966500.0	31206555.0	GSM5509227 r1	0:150 1:150	A:1533392527;C:1543333302;G:4733567814;T:1550956628;N:716229	150	150	1533392527	1543333302	4733567814	1550956628	716229	SRX11676000	SRS9707982	SRA1274130	GEO	Anming Meng Lab, School of Life Science, Tsinghua University	2	0.7668	0.00334	0.06232	0.00092	0.81858	0.99809	0.57209	0.77622	150	150	B	T	mate2 technical by mapping diff	illumina	novaseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	China	2021-08-09	Zygote	Embryo	Whole Organism	All anatomical structures
74222	74222	SRR23610251	SRX19495180	SRS16885249	SRP424410	PRJNA938397	The Effects of Rif1 Loss on Gene Expression During Early Zebrafish Development	GSE226033	Transcriptome Analysis	Deregulated DNA replication is a major contributor to human developmental disorders and cancer yet our understanding of how replication is coordinated with changes in transcription and chromatin structure is limited. Our lab has employed the zebrafish model to investigate the mechanisms driving changes in the replication timing program during development. Previous studies have identified changes in replication timing patterns from the onset of zygotic transcription through gastrulation in zebrafish embryos. The protein Rif1 is crucial for replication timing in a wide range of eukaryotes yet its role in establishing the replication timing program and chromatin structure during early vertebrate development is not well understood. Using Rif1 mutant zebrafish and performing RNA sequencing and whole genome replication timing analysis we found that Rif1 mutants were viable but had a defect in female sex determination. Interestingly Rif1 loss primarily affected DNA replication timing post gastrulation while its impact on transcription was more pronounced during zygotic genome activation. Our results indicate that Rif1 has distinct roles in regulating DNA replication and transcription at different stages of development. Overall design: Quantseq three prime mRNA sequencing data was generated for wild type and rif1 mutant zebrafish embryos at different developmental stages one cell 256 cell Dome Shield Bud and 24 hpf.				1Cell omf201 replicate3	GSM7061827	source name:whole organism\|strain:Tab5\|tissue:whole organism\|developmental stage:Zygote:1cell\|time:0 0.5 hpf\|genotype:rif1 omf201/omf201\|cell cycle phase:Asynchronous\|geo loc name:missing\|collection date:missing	1Cell omf201 replicate3	Raw reads were trimmed with bbmap. Trimmed reads were aligned to the zebrafish genome GRCz11 with STAR. To identify potential internal priming sites in polyA genomic sequences a custom R script was developed and implemented. Once internal priming sites were identified the same script was used to remove reads that mapped to these sites. Reads aligning to 3’ ends of transcripts are then counted using htseq. The 4.3.2 transcript annotation by Lawson et al doi: 10.7554/eLife.55792 was used. Assembly: GRCz11 Supplementary files format and content: Counts.csv has read counts at three prime ends of transcripts assigned to Ensembl gene IDs.	whole organism	Zebrafish embryos were spawned and staged within 10 minutes of fertilization and were subsequently incubated at 28.5°C. Prior to collection all clutches were visually examined to ensure synchronous development and any unfertilized or morphologically abnormal embryos were removed. Batches of whole embryos were rapidly frozen and stored at 80°C for later processing for mRNA.	The mRNA was prepared from whole embryo pools using the RNeasy Mini Kit 493 74104; Qiagen. The QuantSeq libraries were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit for Illumina Lexogen. RNA sequencing was conducted using custom primers on an Illumina Nextseq 500 with High Output chemistry and 75bp single ended reads.	Adult breeding fish were housed in an aquatic animal facility in tanks of ∼30 fish per tank and maintained at 26.5°C with 10 hour light and 14 hour dark cycles.	strain:Tab5\|tissue:whole organism\|developmental stage:Zygote:1cell\|time:0 0.5 hpf\|genotype:rif1 omf201/omf201\|cell cycle phase:Asynchronous	GSM7061827	GSM7061827: 1Cell omf201 replicate3; Danio rerio; RNA Seq	GSM7061827 r1	GSM7061827	1	The mRNA was prepared from whole embryo pools using the RNeasy Mini Kit 493 74104; Qiagen. The QuantSeq libraries were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit for Illumina Lexogen. RNA sequencing was conducted using custom primers on an Illumina Nextseq 500 with High Output chemistry and 75bp single ended reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP424410		8_Mutant_1-cell_S7_R1_001.fastq	fastq	3621239868.0	47647893.0	GSM7061827 r1	0:76 1:0	A:1067635575;C:741686497;G:968439422;T:843432865;N:45509	76	0	1067635575	741686497	968439422	843432865	45509	SRX19495180	SRS16885249	SRA1595486	Sansam Lab, Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation	Sansam Lab, Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation	1	0.80855		0.2144		0.81042		0.63184		76		B		usable mapping rate	illumina	nextseq	3prime	poly_a	lexogen	bulk	unknown	unknown	United States	2023-02-24	Zygote	Embryo	Whole Organism	All anatomical structures
74223	74223	SRR23610252	SRX19495179	SRS16885248	SRP424410	PRJNA938397	The Effects of Rif1 Loss on Gene Expression During Early Zebrafish Development	GSE226033	Transcriptome Analysis	Deregulated DNA replication is a major contributor to human developmental disorders and cancer yet our understanding of how replication is coordinated with changes in transcription and chromatin structure is limited. Our lab has employed the zebrafish model to investigate the mechanisms driving changes in the replication timing program during development. Previous studies have identified changes in replication timing patterns from the onset of zygotic transcription through gastrulation in zebrafish embryos. The protein Rif1 is crucial for replication timing in a wide range of eukaryotes yet its role in establishing the replication timing program and chromatin structure during early vertebrate development is not well understood. Using Rif1 mutant zebrafish and performing RNA sequencing and whole genome replication timing analysis we found that Rif1 mutants were viable but had a defect in female sex determination. Interestingly Rif1 loss primarily affected DNA replication timing post gastrulation while its impact on transcription was more pronounced during zygotic genome activation. Our results indicate that Rif1 has distinct roles in regulating DNA replication and transcription at different stages of development. Overall design: Quantseq three prime mRNA sequencing data was generated for wild type and rif1 mutant zebrafish embryos at different developmental stages one cell 256 cell Dome Shield Bud and 24 hpf.				1Cell omf201 replicate2	GSM7061826	source name:whole organism\|strain:Tab5\|tissue:whole organism\|developmental stage:Zygote:1cell\|time:0 0.5 hpf\|genotype:rif1 omf201/omf201\|cell cycle phase:Asynchronous\|geo loc name:missing\|collection date:missing	1Cell omf201 replicate2	Raw reads were trimmed with bbmap. Trimmed reads were aligned to the zebrafish genome GRCz11 with STAR. To identify potential internal priming sites in polyA genomic sequences a custom R script was developed and implemented. Once internal priming sites were identified the same script was used to remove reads that mapped to these sites. Reads aligning to 3’ ends of transcripts are then counted using htseq. The 4.3.2 transcript annotation by Lawson et al doi: 10.7554/eLife.55792 was used. Assembly: GRCz11 Supplementary files format and content: Counts.csv has read counts at three prime ends of transcripts assigned to Ensembl gene IDs.	whole organism	Zebrafish embryos were spawned and staged within 10 minutes of fertilization and were subsequently incubated at 28.5°C. Prior to collection all clutches were visually examined to ensure synchronous development and any unfertilized or morphologically abnormal embryos were removed. Batches of whole embryos were rapidly frozen and stored at 80°C for later processing for mRNA.	The mRNA was prepared from whole embryo pools using the RNeasy Mini Kit 493 74104; Qiagen. The QuantSeq libraries were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit for Illumina Lexogen. RNA sequencing was conducted using custom primers on an Illumina Nextseq 500 with High Output chemistry and 75bp single ended reads.	Adult breeding fish were housed in an aquatic animal facility in tanks of ∼30 fish per tank and maintained at 26.5°C with 10 hour light and 14 hour dark cycles.	strain:Tab5\|tissue:whole organism\|developmental stage:Zygote:1cell\|time:0 0.5 hpf\|genotype:rif1 omf201/omf201\|cell cycle phase:Asynchronous	GSM7061826	GSM7061826: 1Cell omf201 replicate2; Danio rerio; RNA Seq	GSM7061826 r1	GSM7061826	1	The mRNA was prepared from whole embryo pools using the RNeasy Mini Kit 493 74104; Qiagen. The QuantSeq libraries were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit for Illumina Lexogen. RNA sequencing was conducted using custom primers on an Illumina Nextseq 500 with High Output chemistry and 75bp single ended reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP424410		7_Mutant_1-cell_S6_R1_001.fastq	fastq	4582843472.0	60300572.0	GSM7061826 r1	0:76 1:0	A:1444577852;C:875451218;G:1197297508;T:1065459039;N:57855	76	0	1444577852	875451218	1197297508	1065459039	57855	SRX19495179	SRS16885248	SRA1595486	Sansam Lab, Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation	Sansam Lab, Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation	1	0.73437		0.16929		0.80724		0.61196		76		B		usable mapping rate	illumina	nextseq	3prime	poly_a	lexogen	bulk	unknown	unknown	United States	2023-02-24	Zygote	Embryo	Whole Organism	All anatomical structures
74224	74224	SRR23610253	SRX19495178	SRS16885247	SRP424410	PRJNA938397	The Effects of Rif1 Loss on Gene Expression During Early Zebrafish Development	GSE226033	Transcriptome Analysis	Deregulated DNA replication is a major contributor to human developmental disorders and cancer yet our understanding of how replication is coordinated with changes in transcription and chromatin structure is limited. Our lab has employed the zebrafish model to investigate the mechanisms driving changes in the replication timing program during development. Previous studies have identified changes in replication timing patterns from the onset of zygotic transcription through gastrulation in zebrafish embryos. The protein Rif1 is crucial for replication timing in a wide range of eukaryotes yet its role in establishing the replication timing program and chromatin structure during early vertebrate development is not well understood. Using Rif1 mutant zebrafish and performing RNA sequencing and whole genome replication timing analysis we found that Rif1 mutants were viable but had a defect in female sex determination. Interestingly Rif1 loss primarily affected DNA replication timing post gastrulation while its impact on transcription was more pronounced during zygotic genome activation. Our results indicate that Rif1 has distinct roles in regulating DNA replication and transcription at different stages of development. Overall design: Quantseq three prime mRNA sequencing data was generated for wild type and rif1 mutant zebrafish embryos at different developmental stages one cell 256 cell Dome Shield Bud and 24 hpf.				1Cell omf201 replicate1	GSM7061825	source name:whole organism\|strain:Tab5\|tissue:whole organism\|developmental stage:Zygote:1cell\|time:0 0.5 hpf\|genotype:rif1 omf201/omf201\|cell cycle phase:Asynchronous\|geo loc name:missing\|collection date:missing	1Cell omf201 replicate1	Raw reads were trimmed with bbmap. Trimmed reads were aligned to the zebrafish genome GRCz11 with STAR. To identify potential internal priming sites in polyA genomic sequences a custom R script was developed and implemented. Once internal priming sites were identified the same script was used to remove reads that mapped to these sites. Reads aligning to 3’ ends of transcripts are then counted using htseq. The 4.3.2 transcript annotation by Lawson et al doi: 10.7554/eLife.55792 was used. Assembly: GRCz11 Supplementary files format and content: Counts.csv has read counts at three prime ends of transcripts assigned to Ensembl gene IDs.	whole organism	Zebrafish embryos were spawned and staged within 10 minutes of fertilization and were subsequently incubated at 28.5°C. Prior to collection all clutches were visually examined to ensure synchronous development and any unfertilized or morphologically abnormal embryos were removed. Batches of whole embryos were rapidly frozen and stored at 80°C for later processing for mRNA.	The mRNA was prepared from whole embryo pools using the RNeasy Mini Kit 493 74104; Qiagen. The QuantSeq libraries were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit for Illumina Lexogen. RNA sequencing was conducted using custom primers on an Illumina Nextseq 500 with High Output chemistry and 75bp single ended reads.	Adult breeding fish were housed in an aquatic animal facility in tanks of ∼30 fish per tank and maintained at 26.5°C with 10 hour light and 14 hour dark cycles.	strain:Tab5\|tissue:whole organism\|developmental stage:Zygote:1cell\|time:0 0.5 hpf\|genotype:rif1 omf201/omf201\|cell cycle phase:Asynchronous	GSM7061825	GSM7061825: 1Cell omf201 replicate1; Danio rerio; RNA Seq	GSM7061825 r1	GSM7061825	1	The mRNA was prepared from whole embryo pools using the RNeasy Mini Kit 493 74104; Qiagen. The QuantSeq libraries were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit for Illumina Lexogen. RNA sequencing was conducted using custom primers on an Illumina Nextseq 500 with High Output chemistry and 75bp single ended reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP424410		6_Mutant_1-cell_S5_R1_001.fastq	fastq	4528521028.0	59585803.0	GSM7061825 r1	0:76 1:0	A:1466176270;C:884402015;G:1169232577;T:1008651588;N:58578	76	0	1466176270	884402015	1169232577	1008651588	58578	SRX19495178	SRS16885247	SRA1595486	Sansam Lab, Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation	Sansam Lab, Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation	1	0.74211		0.16681		0.80655		0.62927		76		B		usable mapping rate	illumina	nextseq	3prime	poly_a	lexogen	bulk	unknown	unknown	United States	2023-02-24	Zygote	Embryo	Whole Organism	All anatomical structures
74225	74225	SRR23610254	SRX19495177	SRS16885246	SRP424410	PRJNA938397	The Effects of Rif1 Loss on Gene Expression During Early Zebrafish Development	GSE226033	Transcriptome Analysis	Deregulated DNA replication is a major contributor to human developmental disorders and cancer yet our understanding of how replication is coordinated with changes in transcription and chromatin structure is limited. Our lab has employed the zebrafish model to investigate the mechanisms driving changes in the replication timing program during development. Previous studies have identified changes in replication timing patterns from the onset of zygotic transcription through gastrulation in zebrafish embryos. The protein Rif1 is crucial for replication timing in a wide range of eukaryotes yet its role in establishing the replication timing program and chromatin structure during early vertebrate development is not well understood. Using Rif1 mutant zebrafish and performing RNA sequencing and whole genome replication timing analysis we found that Rif1 mutants were viable but had a defect in female sex determination. Interestingly Rif1 loss primarily affected DNA replication timing post gastrulation while its impact on transcription was more pronounced during zygotic genome activation. Our results indicate that Rif1 has distinct roles in regulating DNA replication and transcription at different stages of development. Overall design: Quantseq three prime mRNA sequencing data was generated for wild type and rif1 mutant zebrafish embryos at different developmental stages one cell 256 cell Dome Shield Bud and 24 hpf.				1Cell wildtype replicate4	GSM7061824	source name:whole organism\|strain:Tab5\|tissue:whole organism\|developmental stage:Zygote:1cell\|time:0 0.5 hpf\|genotype:WT\|cell cycle phase:Asynchronous\|geo loc name:missing\|collection date:missing	1Cell wildtype replicate4	Raw reads were trimmed with bbmap. Trimmed reads were aligned to the zebrafish genome GRCz11 with STAR. To identify potential internal priming sites in polyA genomic sequences a custom R script was developed and implemented. Once internal priming sites were identified the same script was used to remove reads that mapped to these sites. Reads aligning to 3’ ends of transcripts are then counted using htseq. The 4.3.2 transcript annotation by Lawson et al doi: 10.7554/eLife.55792 was used. Assembly: GRCz11 Supplementary files format and content: Counts.csv has read counts at three prime ends of transcripts assigned to Ensembl gene IDs.	whole organism	Zebrafish embryos were spawned and staged within 10 minutes of fertilization and were subsequently incubated at 28.5°C. Prior to collection all clutches were visually examined to ensure synchronous development and any unfertilized or morphologically abnormal embryos were removed. Batches of whole embryos were rapidly frozen and stored at 80°C for later processing for mRNA.	The mRNA was prepared from whole embryo pools using the RNeasy Mini Kit 493 74104; Qiagen. The QuantSeq libraries were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit for Illumina Lexogen. RNA sequencing was conducted using custom primers on an Illumina Nextseq 500 with High Output chemistry and 75bp single ended reads.	Adult breeding fish were housed in an aquatic animal facility in tanks of ∼30 fish per tank and maintained at 26.5°C with 10 hour light and 14 hour dark cycles.	strain:Tab5\|tissue:whole organism\|developmental stage:Zygote:1cell\|time:0 0.5 hpf\|genotype:WT\|cell cycle phase:Asynchronous	GSM7061824	GSM7061824: 1Cell wildtype replicate4; Danio rerio; RNA Seq	GSM7061824 r1	GSM7061824	1	The mRNA was prepared from whole embryo pools using the RNeasy Mini Kit 493 74104; Qiagen. The QuantSeq libraries were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit for Illumina Lexogen. RNA sequencing was conducted using custom primers on an Illumina Nextseq 500 with High Output chemistry and 75bp single ended reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP424410		4_WT_1-cell_S4_R1_001.fastq	fastq	3765358440.0	49544190.0	GSM7061824 r1	0:76 1:0	A:1173776287;C:697987283;G:904980466;T:988566605;N:47799	76	0	1173776287	697987283	904980466	988566605	47799	SRX19495177	SRS16885246	SRA1595486	Sansam Lab, Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation	Sansam Lab, Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation	1	0.8183		0.11227		0.803		0.67181		76		B		usable mapping rate	illumina	nextseq	3prime	poly_a	lexogen	bulk	unknown	unknown	United States	2023-02-24	Zygote	Embryo	Whole Organism	All anatomical structures
74226	74226	SRR23610255	SRX19495176	SRS16885245	SRP424410	PRJNA938397	The Effects of Rif1 Loss on Gene Expression During Early Zebrafish Development	GSE226033	Transcriptome Analysis	Deregulated DNA replication is a major contributor to human developmental disorders and cancer yet our understanding of how replication is coordinated with changes in transcription and chromatin structure is limited. Our lab has employed the zebrafish model to investigate the mechanisms driving changes in the replication timing program during development. Previous studies have identified changes in replication timing patterns from the onset of zygotic transcription through gastrulation in zebrafish embryos. The protein Rif1 is crucial for replication timing in a wide range of eukaryotes yet its role in establishing the replication timing program and chromatin structure during early vertebrate development is not well understood. Using Rif1 mutant zebrafish and performing RNA sequencing and whole genome replication timing analysis we found that Rif1 mutants were viable but had a defect in female sex determination. Interestingly Rif1 loss primarily affected DNA replication timing post gastrulation while its impact on transcription was more pronounced during zygotic genome activation. Our results indicate that Rif1 has distinct roles in regulating DNA replication and transcription at different stages of development. Overall design: Quantseq three prime mRNA sequencing data was generated for wild type and rif1 mutant zebrafish embryos at different developmental stages one cell 256 cell Dome Shield Bud and 24 hpf.				1Cell wildtype replicate3	GSM7061823	source name:whole organism\|strain:Tab5\|tissue:whole organism\|developmental stage:Zygote:1cell\|time:0 0.5 hpf\|genotype:WT\|cell cycle phase:Asynchronous\|geo loc name:missing\|collection date:missing	1Cell wildtype replicate3	Raw reads were trimmed with bbmap. Trimmed reads were aligned to the zebrafish genome GRCz11 with STAR. To identify potential internal priming sites in polyA genomic sequences a custom R script was developed and implemented. Once internal priming sites were identified the same script was used to remove reads that mapped to these sites. Reads aligning to 3’ ends of transcripts are then counted using htseq. The 4.3.2 transcript annotation by Lawson et al doi: 10.7554/eLife.55792 was used. Assembly: GRCz11 Supplementary files format and content: Counts.csv has read counts at three prime ends of transcripts assigned to Ensembl gene IDs.	whole organism	Zebrafish embryos were spawned and staged within 10 minutes of fertilization and were subsequently incubated at 28.5°C. Prior to collection all clutches were visually examined to ensure synchronous development and any unfertilized or morphologically abnormal embryos were removed. Batches of whole embryos were rapidly frozen and stored at 80°C for later processing for mRNA.	The mRNA was prepared from whole embryo pools using the RNeasy Mini Kit 493 74104; Qiagen. The QuantSeq libraries were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit for Illumina Lexogen. RNA sequencing was conducted using custom primers on an Illumina Nextseq 500 with High Output chemistry and 75bp single ended reads.	Adult breeding fish were housed in an aquatic animal facility in tanks of ∼30 fish per tank and maintained at 26.5°C with 10 hour light and 14 hour dark cycles.	strain:Tab5\|tissue:whole organism\|developmental stage:Zygote:1cell\|time:0 0.5 hpf\|genotype:WT\|cell cycle phase:Asynchronous	GSM7061823	GSM7061823: 1Cell wildtype replicate3; Danio rerio; RNA Seq	GSM7061823 r1	GSM7061823	1	The mRNA was prepared from whole embryo pools using the RNeasy Mini Kit 493 74104; Qiagen. The QuantSeq libraries were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit for Illumina Lexogen. RNA sequencing was conducted using custom primers on an Illumina Nextseq 500 with High Output chemistry and 75bp single ended reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP424410		3_WT_1-cell_S3_R1_001.fastq	fastq	4041450328.0	53176978.0	GSM7061823 r1	0:76 1:0	A:1240801068;C:791283858;G:1045235163;T:964078036;N:52203	76	0	1240801068	791283858	1045235163	964078036	52203	SRX19495176	SRS16885245	SRA1595486	Sansam Lab, Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation	Sansam Lab, Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation	1	0.77989		0.19491		0.80697		0.63257		76		B		usable mapping rate	illumina	nextseq	3prime	poly_a	lexogen	bulk	unknown	unknown	United States	2023-02-24	Zygote	Embryo	Whole Organism	All anatomical structures
74227	74227	SRR23610256	SRX19495175	SRS16885244	SRP424410	PRJNA938397	The Effects of Rif1 Loss on Gene Expression During Early Zebrafish Development	GSE226033	Transcriptome Analysis	Deregulated DNA replication is a major contributor to human developmental disorders and cancer yet our understanding of how replication is coordinated with changes in transcription and chromatin structure is limited. Our lab has employed the zebrafish model to investigate the mechanisms driving changes in the replication timing program during development. Previous studies have identified changes in replication timing patterns from the onset of zygotic transcription through gastrulation in zebrafish embryos. The protein Rif1 is crucial for replication timing in a wide range of eukaryotes yet its role in establishing the replication timing program and chromatin structure during early vertebrate development is not well understood. Using Rif1 mutant zebrafish and performing RNA sequencing and whole genome replication timing analysis we found that Rif1 mutants were viable but had a defect in female sex determination. Interestingly Rif1 loss primarily affected DNA replication timing post gastrulation while its impact on transcription was more pronounced during zygotic genome activation. Our results indicate that Rif1 has distinct roles in regulating DNA replication and transcription at different stages of development. Overall design: Quantseq three prime mRNA sequencing data was generated for wild type and rif1 mutant zebrafish embryos at different developmental stages one cell 256 cell Dome Shield Bud and 24 hpf.				1Cell wildtype replicate2	GSM7061822	source name:whole organism\|strain:Tab5\|tissue:whole organism\|developmental stage:Zygote:1cell\|time:0 0.5 hpf\|genotype:WT\|cell cycle phase:Asynchronous\|geo loc name:missing\|collection date:missing	1Cell wildtype replicate2	Raw reads were trimmed with bbmap. Trimmed reads were aligned to the zebrafish genome GRCz11 with STAR. To identify potential internal priming sites in polyA genomic sequences a custom R script was developed and implemented. Once internal priming sites were identified the same script was used to remove reads that mapped to these sites. Reads aligning to 3’ ends of transcripts are then counted using htseq. The 4.3.2 transcript annotation by Lawson et al doi: 10.7554/eLife.55792 was used. Assembly: GRCz11 Supplementary files format and content: Counts.csv has read counts at three prime ends of transcripts assigned to Ensembl gene IDs.	whole organism	Zebrafish embryos were spawned and staged within 10 minutes of fertilization and were subsequently incubated at 28.5°C. Prior to collection all clutches were visually examined to ensure synchronous development and any unfertilized or morphologically abnormal embryos were removed. Batches of whole embryos were rapidly frozen and stored at 80°C for later processing for mRNA.	The mRNA was prepared from whole embryo pools using the RNeasy Mini Kit 493 74104; Qiagen. The QuantSeq libraries were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit for Illumina Lexogen. RNA sequencing was conducted using custom primers on an Illumina Nextseq 500 with High Output chemistry and 75bp single ended reads.	Adult breeding fish were housed in an aquatic animal facility in tanks of ∼30 fish per tank and maintained at 26.5°C with 10 hour light and 14 hour dark cycles.	strain:Tab5\|tissue:whole organism\|developmental stage:Zygote:1cell\|time:0 0.5 hpf\|genotype:WT\|cell cycle phase:Asynchronous	GSM7061822	GSM7061822: 1Cell wildtype replicate2; Danio rerio; RNA Seq	GSM7061822 r1	GSM7061822	1	The mRNA was prepared from whole embryo pools using the RNeasy Mini Kit 493 74104; Qiagen. The QuantSeq libraries were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit for Illumina Lexogen. RNA sequencing was conducted using custom primers on an Illumina Nextseq 500 with High Output chemistry and 75bp single ended reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP424410		2_WT_1-cell_S2_R1_001.fastq	fastq	3988551972.0	52480947.0	GSM7061822 r1	0:76 1:0	A:1205014942;C:751034344;G:983258083;T:1049192801;N:51802	76	0	1205014942	751034344	983258083	1049192801	51802	SRX19495175	SRS16885244	SRA1595486	Sansam Lab, Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation	Sansam Lab, Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation	1	0.81743		0.14811		0.79866		0.61907		76		B		usable mapping rate	illumina	nextseq	3prime	poly_a	lexogen	bulk	unknown	unknown	United States	2023-02-24	Zygote	Embryo	Whole Organism	All anatomical structures
74228	74228	SRR23610257	SRX19495174	SRS16885243	SRP424410	PRJNA938397	The Effects of Rif1 Loss on Gene Expression During Early Zebrafish Development	GSE226033	Transcriptome Analysis	Deregulated DNA replication is a major contributor to human developmental disorders and cancer yet our understanding of how replication is coordinated with changes in transcription and chromatin structure is limited. Our lab has employed the zebrafish model to investigate the mechanisms driving changes in the replication timing program during development. Previous studies have identified changes in replication timing patterns from the onset of zygotic transcription through gastrulation in zebrafish embryos. The protein Rif1 is crucial for replication timing in a wide range of eukaryotes yet its role in establishing the replication timing program and chromatin structure during early vertebrate development is not well understood. Using Rif1 mutant zebrafish and performing RNA sequencing and whole genome replication timing analysis we found that Rif1 mutants were viable but had a defect in female sex determination. Interestingly Rif1 loss primarily affected DNA replication timing post gastrulation while its impact on transcription was more pronounced during zygotic genome activation. Our results indicate that Rif1 has distinct roles in regulating DNA replication and transcription at different stages of development. Overall design: Quantseq three prime mRNA sequencing data was generated for wild type and rif1 mutant zebrafish embryos at different developmental stages one cell 256 cell Dome Shield Bud and 24 hpf.				1Cell wildtype replicate1	GSM7061821	source name:whole organism\|strain:Tab5\|tissue:whole organism\|developmental stage:Zygote:1cell\|time:0 0.5 hpf\|genotype:WT\|cell cycle phase:Asynchronous\|geo loc name:missing\|collection date:missing	1Cell wildtype replicate1	Raw reads were trimmed with bbmap. Trimmed reads were aligned to the zebrafish genome GRCz11 with STAR. To identify potential internal priming sites in polyA genomic sequences a custom R script was developed and implemented. Once internal priming sites were identified the same script was used to remove reads that mapped to these sites. Reads aligning to 3’ ends of transcripts are then counted using htseq. The 4.3.2 transcript annotation by Lawson et al doi: 10.7554/eLife.55792 was used. Assembly: GRCz11 Supplementary files format and content: Counts.csv has read counts at three prime ends of transcripts assigned to Ensembl gene IDs.	whole organism	Zebrafish embryos were spawned and staged within 10 minutes of fertilization and were subsequently incubated at 28.5°C. Prior to collection all clutches were visually examined to ensure synchronous development and any unfertilized or morphologically abnormal embryos were removed. Batches of whole embryos were rapidly frozen and stored at 80°C for later processing for mRNA.	The mRNA was prepared from whole embryo pools using the RNeasy Mini Kit 493 74104; Qiagen. The QuantSeq libraries were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit for Illumina Lexogen. RNA sequencing was conducted using custom primers on an Illumina Nextseq 500 with High Output chemistry and 75bp single ended reads.	Adult breeding fish were housed in an aquatic animal facility in tanks of ∼30 fish per tank and maintained at 26.5°C with 10 hour light and 14 hour dark cycles.	strain:Tab5\|tissue:whole organism\|developmental stage:Zygote:1cell\|time:0 0.5 hpf\|genotype:WT\|cell cycle phase:Asynchronous	GSM7061821	GSM7061821: 1Cell wildtype replicate1; Danio rerio; RNA Seq	GSM7061821 r1	GSM7061821	1	The mRNA was prepared from whole embryo pools using the RNeasy Mini Kit 493 74104; Qiagen. The QuantSeq libraries were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit for Illumina Lexogen. RNA sequencing was conducted using custom primers on an Illumina Nextseq 500 with High Output chemistry and 75bp single ended reads.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP424410		1_WT_1-cell_S1_R1_001.fastq	fastq	4702418528.0	61873928.0	GSM7061821 r1	0:76 1:0	A:1464895616;C:837079133;G:1126018680;T:1274364821;N:60278	76	0	1464895616	837079133	1126018680	1274364821	60278	SRX19495174	SRS16885243	SRA1595486	Sansam Lab, Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation	Sansam Lab, Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation	1	0.80236		0.07809		0.80515		0.65308		76		B		usable mapping rate	illumina	nextseq	3prime	poly_a	lexogen	bulk	unknown	unknown	United States	2023-02-24	Zygote	Embryo	Whole Organism	All anatomical structures

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