metadata: run_metadata: 38 rows where technology = "bulk", tissue_curation = "Oocyte" and tissue_curation

38 rows where technology = "bulk", tissue_curation = "Oocyte" and tissue_curation_coarse = "Reproductive System"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.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
30755	30755	SRR28348921	SRX23954975	SRS20755396	SRP495323	PRJNA1088158	Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.	GSE261646	Transcriptome Analysis	The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…	pubmed:39302832	Zebrafish Oocyte Stage IV rep2	GSM8147872	source name:Oocyte\|tissue:Oocyte\|developmental stage:Stage IV\|genotype:AB TF and TLF\|geo loc name:missing\|collection date:missing	Zebrafish Oocyte Stage IV rep2	Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates	Oocyte		Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.	tissue:Oocyte\|developmental stage:Stage IV\|genotype:AB TF and TLF	GSM8147872	GSM8147872: Zebrafish Oocyte Stage IV rep2; Danio rerio; RNA Seq	GSM8147872 r1	GSM8147872	1	Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP495323		Z_oocyte_stage_4_2_Pa.fastq	fastq	2456514332.0	32322557.0	GSM8147872 r1	0:76	A:588246161;C:609187233;G:593122683;T:665837765;N:120490	76		588246161	609187233	593122683	665837765	120490	SRX23954975	SRS20755396	SRA1824599	Computational Biology, Stowers Institute for Medical Research	Computational Biology, Stowers Institute for Medical Research												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2024-03-14	Multi-stage	Embryo	Oocyte	Reproductive System
30756	30756	SRR28348922	SRX23954974	SRS20755395	SRP495323	PRJNA1088158	Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.	GSE261646	Transcriptome Analysis	The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…	pubmed:39302832	Zebrafish Oocyte Stage IV rep1	GSM8147871	source name:Oocyte\|tissue:Oocyte\|developmental stage:Stage IV\|genotype:AB TF and TLF\|geo loc name:missing\|collection date:missing	Zebrafish Oocyte Stage IV rep1	Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates	Oocyte		Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.	tissue:Oocyte\|developmental stage:Stage IV\|genotype:AB TF and TLF	GSM8147871	GSM8147871: Zebrafish Oocyte Stage IV rep1; Danio rerio; RNA Seq	GSM8147871 r1	GSM8147871	1	Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP495323		Z_oocyte_stage_4_1_Pa.fastq	fastq	2650784696.0	34878746.0	GSM8147871 r1	0:76	A:649971632;C:640667370;G:632570967;T:727447552;N:127175	76		649971632	640667370	632570967	727447552	127175	SRX23954974	SRS20755395	SRA1824599	Computational Biology, Stowers Institute for Medical Research	Computational Biology, Stowers Institute for Medical Research												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2024-03-14	Multi-stage	Embryo	Oocyte	Reproductive System
30757	30757	SRR28348923	SRX23954973	SRS20755394	SRP495323	PRJNA1088158	Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.	GSE261646	Transcriptome Analysis	The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…	pubmed:39302832	Zebrafish Oocyte Stage III rep2	GSM8147870	source name:Oocyte\|tissue:Oocyte\|developmental stage:Stage III\|genotype:AB TF and TLF\|geo loc name:missing\|collection date:missing	Zebrafish Oocyte Stage III rep2	Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates	Oocyte		Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.	tissue:Oocyte\|developmental stage:Stage III\|genotype:AB TF and TLF	GSM8147870	GSM8147870: Zebrafish Oocyte Stage III rep2; Danio rerio; RNA Seq	GSM8147870 r1	GSM8147870	1	Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP495323		Z_oocyte_stage_3_2_Pa.fastq	fastq	2809957956.0	36973131.0	GSM8147870 r1	0:76	A:679041537;C:690924547;G:702857353;T:736996218;N:138301	76		679041537	690924547	702857353	736996218	138301	SRX23954973	SRS20755394	SRA1824599	Computational Biology, Stowers Institute for Medical Research	Computational Biology, Stowers Institute for Medical Research												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2024-03-14	Multi-stage	Embryo	Oocyte	Reproductive System
30758	30758	SRR28348924	SRX23954972	SRS20755393	SRP495323	PRJNA1088158	Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.	GSE261646	Transcriptome Analysis	The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…	pubmed:39302832	Zebrafish Oocyte Stage III rep1	GSM8147869	source name:Oocyte\|tissue:Oocyte\|developmental stage:Stage III\|genotype:AB TF and TLF\|geo loc name:missing\|collection date:missing	Zebrafish Oocyte Stage III rep1	Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates	Oocyte		Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.	tissue:Oocyte\|developmental stage:Stage III\|genotype:AB TF and TLF	GSM8147869	GSM8147869: Zebrafish Oocyte Stage III rep1; Danio rerio; RNA Seq	GSM8147869 r1	GSM8147869	1	Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP495323		Z_oocyte_stage_3_1_Pa.fastq	fastq	2828372376.0	37215426.0	GSM8147869 r1	0:76	A:701751055;C:680571938;G:664212213;T:781698241;N:138929	76		701751055	680571938	664212213	781698241	138929	SRX23954972	SRS20755393	SRA1824599	Computational Biology, Stowers Institute for Medical Research	Computational Biology, Stowers Institute for Medical Research												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2024-03-14	Multi-stage	Embryo	Oocyte	Reproductive System
30759	30759	SRR28348925	SRX23954971	SRS20755392	SRP495323	PRJNA1088158	Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.	GSE261646	Transcriptome Analysis	The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…	pubmed:39302832	Zebrafish Oocyte Stage II rep2	GSM8147868	source name:Oocyte\|tissue:Oocyte\|developmental stage:Stage II\|genotype:AB TF and TLF\|geo loc name:missing\|collection date:missing	Zebrafish Oocyte Stage II rep2	Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates	Oocyte		Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.	tissue:Oocyte\|developmental stage:Stage II\|genotype:AB TF and TLF	GSM8147868	GSM8147868: Zebrafish Oocyte Stage II rep2; Danio rerio; RNA Seq	GSM8147868 r1	GSM8147868	1	Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP495323		Z_oocyte_stage_2_2_Pa.fastq	fastq	2837652432.0	37337532.0	GSM8147868 r1	0:76	A:698931608;C:681467909;G:683751172;T:773364392;N:137351	76		698931608	681467909	683751172	773364392	137351	SRX23954971	SRS20755392	SRA1824599	Computational Biology, Stowers Institute for Medical Research	Computational Biology, Stowers Institute for Medical Research												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2024-03-14	Multi-stage	Embryo	Oocyte	Reproductive System
30760	30760	SRR28348926	SRX23954970	SRS20755391	SRP495323	PRJNA1088158	Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.	GSE261646	Transcriptome Analysis	The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…	pubmed:39302832	Zebrafish Oocyte Stage II rep1	GSM8147867	source name:Oocyte\|tissue:Oocyte\|developmental stage:Stage II\|genotype:AB TF and TLF\|geo loc name:missing\|collection date:missing	Zebrafish Oocyte Stage II rep1	Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates	Oocyte		Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.	tissue:Oocyte\|developmental stage:Stage II\|genotype:AB TF and TLF	GSM8147867	GSM8147867: Zebrafish Oocyte Stage II rep1; Danio rerio; RNA Seq	GSM8147867 r1	GSM8147867	1	Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP495323		Z_oocyte_stage_2_1_Pa.fastq	fastq	3360126820.0	44212195.0	GSM8147867 r1	0:76	A:829333798;C:802089215;G:804982077;T:923557236;N:164494	76		829333798	802089215	804982077	923557236	164494	SRX23954970	SRS20755391	SRA1824599	Computational Biology, Stowers Institute for Medical Research	Computational Biology, Stowers Institute for Medical Research												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2024-03-14	Multi-stage	Embryo	Oocyte	Reproductive System
30761	30761	SRR28348927	SRX23954969	SRS20755390	SRP495323	PRJNA1088158	Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.	GSE261646	Transcriptome Analysis	The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…	pubmed:39302832	Zebrafish Oocyte Stage I rep2	GSM8147866	source name:Oocyte\|tissue:Oocyte\|developmental stage:Stage I\|genotype:AB TF and TLF\|geo loc name:missing\|collection date:missing	Zebrafish Oocyte Stage I rep2	Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates	Oocyte		Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.	tissue:Oocyte\|developmental stage:Stage I\|genotype:AB TF and TLF	GSM8147866	GSM8147866: Zebrafish Oocyte Stage I rep2; Danio rerio; RNA Seq	GSM8147866 r1	GSM8147866	1	Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP495323		Z_oocyte_stage_1_2_Pa.fastq	fastq	2739674220.0	36048345.0	GSM8147866 r1	0:76	A:653441701;C:681445567;G:663740568;T:740918288;N:128096	76		653441701	681445567	663740568	740918288	128096	SRX23954969	SRS20755390	SRA1824599	Computational Biology, Stowers Institute for Medical Research	Computational Biology, Stowers Institute for Medical Research												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2024-03-14	Multi-stage	Embryo	Oocyte	Reproductive System
30762	30762	SRR28348928	SRX23954968	SRS20755389	SRP495323	PRJNA1088158	Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.	GSE261646	Transcriptome Analysis	The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…	pubmed:39302832	Zebrafish Oocyte Stage I rep1	GSM8147865	source name:Oocyte\|tissue:Oocyte\|developmental stage:Stage I\|genotype:AB TF and TLF\|geo loc name:missing\|collection date:missing	Zebrafish Oocyte Stage I rep1	Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates	Oocyte		Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.	tissue:Oocyte\|developmental stage:Stage I\|genotype:AB TF and TLF	GSM8147865	GSM8147865: Zebrafish Oocyte Stage I rep1; Danio rerio; RNA Seq	GSM8147865 r1	GSM8147865	1	Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP495323		Z_oocyte_stage_1_1_Pa.fastq	fastq	3348831852.0	44063577.0	GSM8147865 r1	0:76	A:815134657;C:817210346;G:809175239;T:907149915;N:161695	76		815134657	817210346	809175239	907149915	161695	SRX23954968	SRS20755389	SRA1824599	Computational Biology, Stowers Institute for Medical Research	Computational Biology, Stowers Institute for Medical Research												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2024-03-14	Multi-stage	Embryo	Oocyte	Reproductive System
63340	63340	SRR13729837	SRX10117846	SRS8272547	SRP306811	PRJNA702290	RNA Seq analysis of localization along animal vegetal axis of Danio rerio	GSE166917	Transcriptome Analysis	Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of …	pubmed:35752299	Oocyte 4E Danio	GSM5088021	tissue:Oocyte 4E\|segment:E last vegetal\|cell type:Oocyte\|oocyte id:4	Oocyte 4E Danio	Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.	Oocyte 4E		Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	segment:E last vegetal\|cell type:Oocyte\|oocyte id:4	GSM5088021	GSM5088021: Oocyte 4E Danio; Danio rerio; RNA Seq	GSM5088021		1	Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	GEO Accession:GSM5088021	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306811		4B5_1_sequence.fastq.gz 4B5_2_sequence.fastq.gz	fastq fastq	4152498238.0	26122638.0	GSM5088021 r1	0:79.49 1:79.47	A:1027163417;C:1014220497;G:1089779374;T:1018004142;N:3330808	79	79	1027163417	1014220497	1089779374	1018004142	3330808	SRX10117846	SRS8272547	SRA1197056	GEO	Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.	2	0.91753	0.91112	0.02745	0.02398	0.80996	0.81292	0.50181	0.50039	80	80	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	lexogen	bulk	bulk	bulk	Czech Republic	2021-02-17	Zygote	Embryo	Oocyte	Reproductive System
63341	63341	SRR13729836	SRX10117845	SRS8272546	SRP306811	PRJNA702290	RNA Seq analysis of localization along animal vegetal axis of Danio rerio	GSE166917	Transcriptome Analysis	Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of …	pubmed:35752299	Oocyte 4C Danio	GSM5088020	tissue:Oocyte 4C\|segment:C\|cell type:Oocyte\|oocyte id:4	Oocyte 4C Danio	Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.	Oocyte 4C		Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	segment:C\|cell type:Oocyte\|oocyte id:4	GSM5088020	GSM5088020: Oocyte 4C Danio; Danio rerio; RNA Seq	GSM5088020		1	Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	GEO Accession:GSM5088020	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306811		4B3_1_sequence.fastq.gz 4B3_2_sequence.fastq.gz	fastq fastq	4303501885.0	27073674.0	GSM5088020 r1	0:79.48 1:79.47	A:1081539300;C:1029641993;G:1108664145;T:1080227921;N:3428526	79	79	1081539300	1029641993	1108664145	1080227921	3428526	SRX10117845	SRS8272546	SRA1197056	GEO	Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.	2	0.93052	0.92329	0.0289	0.02632	0.80728	0.8086	0.48613	0.49318	79	79	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	lexogen	bulk	bulk	bulk	Czech Republic	2021-02-17	Zygote	Embryo	Oocyte	Reproductive System
63342	63342	SRR13729835	SRX10117844	SRS8272545	SRP306811	PRJNA702290	RNA Seq analysis of localization along animal vegetal axis of Danio rerio	GSE166917	Transcriptome Analysis	Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of …	pubmed:35752299	Oocyte 4B Danio	GSM5088019	tissue:Oocyte 4B\|segment:B\|cell type:Oocyte\|oocyte id:4	Oocyte 4B Danio	Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.	Oocyte 4B		Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	segment:B\|cell type:Oocyte\|oocyte id:4	GSM5088019	GSM5088019: Oocyte 4B Danio; Danio rerio; RNA Seq	GSM5088019		1	Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	GEO Accession:GSM5088019	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306811		4B2_1_sequence.fastq.gz 4B2_2_sequence.fastq.gz	fastq fastq	4568445606.0	28740891.0	GSM5088019 r1	0:79.48 1:79.47	A:1129548614;C:1110728719;G:1196533300;T:1127950040;N:3684933	79	79	1129548614	1110728719	1196533300	1127950040	3684933	SRX10117844	SRS8272545	SRA1197056	GEO	Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.	2	0.93047	0.91851	0.03423	0.02988	0.809	0.81117	0.49528	0.49857	80	80	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	lexogen	bulk	bulk	bulk	Czech Republic	2021-02-17	Zygote	Embryo	Oocyte	Reproductive System
63343	63343	SRR13729834	SRX10117843	SRS8272544	SRP306811	PRJNA702290	RNA Seq analysis of localization along animal vegetal axis of Danio rerio	GSE166917	Transcriptome Analysis	Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of …	pubmed:35752299	Oocyte 4A Danio	GSM5088018	tissue:Oocyte 4A\|segment:A first animal\|cell type:Oocyte\|oocyte id:4	Oocyte 4A Danio	Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.	Oocyte 4A		Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	segment:A first animal\|cell type:Oocyte\|oocyte id:4	GSM5088018	GSM5088018: Oocyte 4A Danio; Danio rerio; RNA Seq	GSM5088018		1	Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	GEO Accession:GSM5088018	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306811		4B1_1_sequence.fastq.gz 4B1_2_sequence.fastq.gz	fastq fastq	3817977815.0	24018320.0	GSM5088018 r1	0:79.49 1:79.47	A:963219571;C:910978829;G:981236983;T:959479009;N:3063423	79	79	963219571	910978829	981236983	959479009	3063423	SRX10117843	SRS8272544	SRA1197056	GEO	Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.	2	0.91985	0.91378	0.02505	0.02244	0.82487	0.82662	0.49099	0.48748	79	80	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	lexogen	bulk	bulk	bulk	Czech Republic	2021-02-17	Zygote	Embryo	Oocyte	Reproductive System
63344	63344	SRR13729833	SRX10117842	SRS8272543	SRP306811	PRJNA702290	RNA Seq analysis of localization along animal vegetal axis of Danio rerio	GSE166917	Transcriptome Analysis	Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of …	pubmed:35752299	Oocyte 3E Danio	GSM5088017	tissue:Oocyte 3E\|segment:E last vegetal\|cell type:Oocyte\|oocyte id:3	Oocyte 3E Danio	Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.	Oocyte 3E		Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	segment:E last vegetal\|cell type:Oocyte\|oocyte id:3	GSM5088017	GSM5088017: Oocyte 3E Danio; Danio rerio; RNA Seq	GSM5088017		1	Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	GEO Accession:GSM5088017	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306811		3B5_1_sequence.fastq.gz 3B5_2_sequence.fastq.gz	fastq fastq	4473509143.0	28141276.0	GSM5088017 r1	0:79.48 1:79.48	A:1097552285;C:1100434019;G:1180150633;T:1091792820;N:3579386	79	79	1097552285	1100434019	1180150633	1091792820	3579386	SRX10117842	SRS8272543	SRA1197056	GEO	Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.	2	0.91717	0.91194	0.03477	0.02973	0.81714	0.81789	0.50164	0.50948	80	79	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	lexogen	bulk	bulk	bulk	Czech Republic	2021-02-17	Zygote	Embryo	Oocyte	Reproductive System
63345	63345	SRR13729832	SRX10117841	SRS8272542	SRP306811	PRJNA702290	RNA Seq analysis of localization along animal vegetal axis of Danio rerio	GSE166917	Transcriptome Analysis	Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of …	pubmed:35752299	Oocyte 3D Danio	GSM5088016	tissue:Oocyte 3D\|segment:D\|cell type:Oocyte\|oocyte id:3	Oocyte 3D Danio	Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.	Oocyte 3D		Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	segment:D\|cell type:Oocyte\|oocyte id:3	GSM5088016	GSM5088016: Oocyte 3D Danio; Danio rerio; RNA Seq	GSM5088016		1	Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	GEO Accession:GSM5088016	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306811		3B4_1_sequence.fastq.gz 3B4_2_sequence.fastq.gz	fastq fastq	3795326466.0	23875658.0	GSM5088016 r1	0:79.48 1:79.48	A:920554794;C:947025114;G:1013528010;T:911203644;N:3014904	79	79	920554794	947025114	1013528010	911203644	3014904	SRX10117841	SRS8272542	SRA1197056	GEO	Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.	2	0.91408	0.91455	0.037	0.03125	0.82166	0.82426	0.53064	0.53695	78	80	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	lexogen	bulk	bulk	bulk	Czech Republic	2021-02-17	Zygote	Embryo	Oocyte	Reproductive System
63346	63346	SRR13729831	SRX10117840	SRS8272541	SRP306811	PRJNA702290	RNA Seq analysis of localization along animal vegetal axis of Danio rerio	GSE166917	Transcriptome Analysis	Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of …	pubmed:35752299	Oocyte 3C Danio	GSM5088015	tissue:Oocyte 3C\|segment:C\|cell type:Oocyte\|oocyte id:3	Oocyte 3C Danio	Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.	Oocyte 3C		Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	segment:C\|cell type:Oocyte\|oocyte id:3	GSM5088015	GSM5088015: Oocyte 3C Danio; Danio rerio; RNA Seq	GSM5088015		1	Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	GEO Accession:GSM5088015	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306811		3B3_1_sequence.fastq.gz 3B3_2_sequence.fastq.gz	fastq fastq	4384361494.0	27581768.0	GSM5088015 r1	0:79.49 1:79.47	A:1098383452;C:1051673687;G:1134807000;T:1095992230;N:3505125	79	79	1098383452	1051673687	1134807000	1095992230	3505125	SRX10117840	SRS8272541	SRA1197056	GEO	Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.	2	0.92005	0.91267	0.02325	0.02051	0.84593	0.84652	0.47588	0.47964	80	79	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	lexogen	bulk	bulk	bulk	Czech Republic	2021-02-17	Zygote	Embryo	Oocyte	Reproductive System
63347	63347	SRR13729830	SRX10117839	SRS8272540	SRP306811	PRJNA702290	RNA Seq analysis of localization along animal vegetal axis of Danio rerio	GSE166917	Transcriptome Analysis	Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of …	pubmed:35752299	Oocyte 3A Danio	GSM5088014	tissue:Oocyte 3A\|segment:A first animal\|cell type:Oocyte\|oocyte id:3	Oocyte 3A Danio	Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.	Oocyte 3A		Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	segment:A first animal\|cell type:Oocyte\|oocyte id:3	GSM5088014	GSM5088014: Oocyte 3A Danio; Danio rerio; RNA Seq	GSM5088014		1	Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	GEO Accession:GSM5088014	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306811		3B1_1_sequence.fastq.gz 3B1_2_sequence.fastq.gz	fastq fastq	3411652124.0	21461889.0	GSM5088014 r1	0:79.49 1:79.47	A:845211429;C:831298444;G:892682122;T:839715401;N:2744728	79	79	845211429	831298444	892682122	839715401	2744728	SRX10117839	SRS8272540	SRA1197056	GEO	Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.	2	0.91312	0.90785	0.03043	0.03046	0.81227	0.81412	0.47591	0.48217	80	80	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	lexogen	bulk	bulk	bulk	Czech Republic	2021-02-17	Zygote	Embryo	Oocyte	Reproductive System
63348	63348	SRR13729829	SRX10117838	SRS8272539	SRP306811	PRJNA702290	RNA Seq analysis of localization along animal vegetal axis of Danio rerio	GSE166917	Transcriptome Analysis	Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of …	pubmed:35752299	Oocyte 2D Danio	GSM5088013	tissue:Oocyte 2D\|segment:D\|cell type:Oocyte\|oocyte id:2	Oocyte 2D Danio	Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.	Oocyte 2D		Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	segment:D\|cell type:Oocyte\|oocyte id:2	GSM5088013	GSM5088013: Oocyte 2D Danio; Danio rerio; RNA Seq	GSM5088013		1	Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	GEO Accession:GSM5088013	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306811		2B4_1_sequence.fastq.gz 2B4_2_sequence.fastq.gz	fastq fastq	4315673164.0	27151788.0	GSM5088013 r1	0:79.48 1:79.47	A:1054372456;C:1069138368;G:1139564933;T:1049164939;N:3432468	79	79	1054372456	1069138368	1139564933	1049164939	3432468	SRX10117838	SRS8272539	SRA1197056	GEO	Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.	2	0.92682	0.91833	0.0285	0.02736	0.83128	0.83386	0.49243	0.48841	80	80	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	lexogen	bulk	bulk	bulk	Czech Republic	2021-02-17	Zygote	Embryo	Oocyte	Reproductive System
63349	63349	SRR13729828	SRX10117837	SRS8272538	SRP306811	PRJNA702290	RNA Seq analysis of localization along animal vegetal axis of Danio rerio	GSE166917	Transcriptome Analysis	Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of …	pubmed:35752299	Oocyte 2C Danio	GSM5088012	tissue:Oocyte 2C\|segment:C\|cell type:Oocyte\|oocyte id:2	Oocyte 2C Danio	Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.	Oocyte 2C		Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	segment:C\|cell type:Oocyte\|oocyte id:2	GSM5088012	GSM5088012: Oocyte 2C Danio; Danio rerio; RNA Seq	GSM5088012		1	Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	GEO Accession:GSM5088012	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306811		2B3_1_sequence.fastq.gz 2B3_2_sequence.fastq.gz	fastq fastq	2940179416.0	18498584.0	GSM5088012 r1	0:79.48 1:79.46	A:706640732;C:738153613;G:787676271;T:705356358;N:2352442	79	79	706640732	738153613	787676271	705356358	2352442	SRX10117837	SRS8272538	SRA1197056	GEO	Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.	2	0.91412	0.90752	0.03266	0.03078	0.81294	0.81544	0.48861	0.50372	80	80	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	lexogen	bulk	bulk	bulk	Czech Republic	2021-02-17	Zygote	Embryo	Oocyte	Reproductive System
63350	63350	SRR13729827	SRX10117836	SRS8272537	SRP306811	PRJNA702290	RNA Seq analysis of localization along animal vegetal axis of Danio rerio	GSE166917	Transcriptome Analysis	Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of …	pubmed:35752299	Oocyte 2B Danio	GSM5088011	tissue:Oocyte 2B\|segment:B\|cell type:Oocyte\|oocyte id:2	Oocyte 2B Danio	Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.	Oocyte 2B		Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	segment:B\|cell type:Oocyte\|oocyte id:2	GSM5088011	GSM5088011: Oocyte 2B Danio; Danio rerio; RNA Seq	GSM5088011		1	Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	GEO Accession:GSM5088011	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306811		2B2_1_sequence.fastq.gz 2B2_2_sequence.fastq.gz	fastq fastq	4697262619.0	29554887.0	GSM5088011 r1	0:79.47 1:79.46	A:1144577689;C:1159225165;G:1242203382;T:1147513885;N:3742498	79	79	1144577689	1159225165	1242203382	1147513885	3742498	SRX10117836	SRS8272537	SRA1197056	GEO	Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.	2	0.92868	0.92039	0.03005	0.02833	0.83043	0.83201	0.48282	0.4842	80	79	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	lexogen	bulk	bulk	bulk	Czech Republic	2021-02-17	Zygote	Embryo	Oocyte	Reproductive System
63351	63351	SRR13729826	SRX10117835	SRS8272536	SRP306811	PRJNA702290	RNA Seq analysis of localization along animal vegetal axis of Danio rerio	GSE166917	Transcriptome Analysis	Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of …	pubmed:35752299	Oocyte 2A Danio	GSM5088010	tissue:Oocyte 2A\|segment:A first animal\|cell type:Oocyte\|oocyte id:2	Oocyte 2A Danio	Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.	Oocyte 2A		Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	segment:A first animal\|cell type:Oocyte\|oocyte id:2	GSM5088010	GSM5088010: Oocyte 2A Danio; Danio rerio; RNA Seq	GSM5088010		1	Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	GEO Accession:GSM5088010	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306811		2B1_1_sequence.fastq.gz 2B1_2_sequence.fastq.gz	fastq fastq	4258170980.0	26788207.0	GSM5088010 r1	0:79.49 1:79.47	A:1030159627;C:1059437908;G:1140549602;T:1024611576;N:3412267	79	79	1030159627	1059437908	1140549602	1024611576	3412267	SRX10117835	SRS8272536	SRA1197056	GEO	Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.	2	0.90756	0.90301	0.03357	0.03114	0.82246	0.82353	0.48748	0.48875	78	80	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	lexogen	bulk	bulk	bulk	Czech Republic	2021-02-17	Zygote	Embryo	Oocyte	Reproductive System
63352	63352	SRR13729825	SRX10117834	SRS8272535	SRP306811	PRJNA702290	RNA Seq analysis of localization along animal vegetal axis of Danio rerio	GSE166917	Transcriptome Analysis	Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of …	pubmed:35752299	Oocyte 1E Danio	GSM5088009	tissue:Oocyte 1E\|segment:E last vegetal\|cell type:Oocyte\|oocyte id:1	Oocyte 1E Danio	Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.	Oocyte 1E		Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	segment:E last vegetal\|cell type:Oocyte\|oocyte id:1	GSM5088009	GSM5088009: Oocyte 1E Danio; Danio rerio; RNA Seq	GSM5088009		1	Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	GEO Accession:GSM5088009	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306811		1B5_1_sequence.fastq.gz 1B5_2_sequence.fastq.gz	fastq fastq	1540315534.0	9689873.0	GSM5088009 r1	0:79.49 1:79.47	A:379857715;C:379231426;G:406324313;T:373666639;N:1235441	79	79	379857715	379231426	406324313	373666639	1235441	SRX10117834	SRS8272535	SRA1197056	GEO	Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.	2	0.90259	0.90038	0.02393	0.02279	0.82538	0.828	0.50474	0.50554	80	80	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	lexogen	bulk	bulk	bulk	Czech Republic	2021-02-17	Zygote	Embryo	Oocyte	Reproductive System
63353	63353	SRR13729824	SRX10117833	SRS8272534	SRP306811	PRJNA702290	RNA Seq analysis of localization along animal vegetal axis of Danio rerio	GSE166917	Transcriptome Analysis	Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of …	pubmed:35752299	Oocyte 1D Danio	GSM5088008	tissue:Oocyte 1D\|segment:D\|cell type:Oocyte\|oocyte id:1	Oocyte 1D Danio	Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.	Oocyte 1D		Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	segment:D\|cell type:Oocyte\|oocyte id:1	GSM5088008	GSM5088008: Oocyte 1D Danio; Danio rerio; RNA Seq	GSM5088008		1	Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	GEO Accession:GSM5088008	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306811		1B4_1_sequence.fastq.gz 1B4_2_sequence.fastq.gz	fastq fastq	962876607.0	6058091.0	GSM5088008 r1	0:79.47 1:79.47	A:229221564;C:244601669;G:261639054;T:226646308;N:768012	79	79	229221564	244601669	261639054	226646308	768012	SRX10117833	SRS8272534	SRA1197056	GEO	Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.	2	0.90756	0.90342	0.03356	0.03192	0.81418	0.81588	0.53647	0.53381	80	80	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	lexogen	bulk	bulk	bulk	Czech Republic	2021-02-17	Zygote	Embryo	Oocyte	Reproductive System
63354	63354	SRR13729823	SRX10117832	SRS8272532	SRP306811	PRJNA702290	RNA Seq analysis of localization along animal vegetal axis of Danio rerio	GSE166917	Transcriptome Analysis	Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of …	pubmed:35752299	Oocyte 1C Danio	GSM5088007	tissue:Oocyte 1C\|segment:C\|cell type:Oocyte\|oocyte id:1	Oocyte 1C Danio	Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.	Oocyte 1C		Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	segment:C\|cell type:Oocyte\|oocyte id:1	GSM5088007	GSM5088007: Oocyte 1C Danio; Danio rerio; RNA Seq	GSM5088007		1	Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	GEO Accession:GSM5088007	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306811		1B3_1_sequence.fastq.gz 1B3_2_sequence.fastq.gz	fastq fastq	1582022971.0	9951749.0	GSM5088007 r1	0:79.49 1:79.48	A:396538041;C:379495578;G:410865933;T:393855027;N:1268392	79	79	396538041	379495578	410865933	393855027	1268392	SRX10117832	SRS8272532	SRA1197056	GEO	Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.	2	0.93154	0.91852	0.03066	0.02748	0.81874	0.82037	0.50484	0.50755	80	78	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	lexogen	bulk	bulk	bulk	Czech Republic	2021-02-17	Zygote	Embryo	Oocyte	Reproductive System
63355	63355	SRR13729822	SRX10117831	SRS8272533	SRP306811	PRJNA702290	RNA Seq analysis of localization along animal vegetal axis of Danio rerio	GSE166917	Transcriptome Analysis	Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of …	pubmed:35752299	Oocyte 1B Danio	GSM5088006	tissue:Oocyte 1B\|segment:B\|cell type:Oocyte\|oocyte id:1	Oocyte 1B Danio	Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.	Oocyte 1B		Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	segment:B\|cell type:Oocyte\|oocyte id:1	GSM5088006	GSM5088006: Oocyte 1B Danio; Danio rerio; RNA Seq	GSM5088006		1	Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	GEO Accession:GSM5088006	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306811		1B2_1_sequence.fastq.gz 1B2_2_sequence.fastq.gz	fastq fastq	1673988669.0	10530092.0	GSM5088006 r1	0:79.49 1:79.48	A:422626348;C:401664830;G:430984922;T:417384157;N:1328412	79	79	422626348	401664830	430984922	417384157	1328412	SRX10117831	SRS8272533	SRA1197056	GEO	Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.	2	0.92018	0.91786	0.03334	0.02831	0.82217	0.82359	0.49692	0.49869	79	80	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	lexogen	bulk	bulk	bulk	Czech Republic	2021-02-17	Zygote	Embryo	Oocyte	Reproductive System
63356	63356	SRR13729821	SRX10117830	SRS8272531	SRP306811	PRJNA702290	RNA Seq analysis of localization along animal vegetal axis of Danio rerio	GSE166917	Transcriptome Analysis	Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of …	pubmed:35752299	Oocyte 1A Danio	GSM5088005	tissue:Oocyte 1A\|segment:A first animal\|cell type:Oocyte\|oocyte id:1	Oocyte 1A Danio	Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.	Oocyte 1A		Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	segment:A first animal\|cell type:Oocyte\|oocyte id:1	GSM5088005	GSM5088005: Oocyte 1A Danio; Danio rerio; RNA Seq	GSM5088005		1	Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.	GEO Accession:GSM5088005	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP306811		1B1_1_sequence.fastq.gz 1B1_2_sequence.fastq.gz	fastq fastq	2267520035.0	14263997.0	GSM5088005 r1	0:79.47 1:79.49	A:545496147;C:565118612;G:611364916;T:543726981;N:1813379	79	79	545496147	565118612	611364916	543726981	1813379	SRX10117830	SRS8272531	SRA1197056	GEO	Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.	2	0.93336	0.92007	0.06438	0.05136	0.82349	0.82483	0.54418	0.55879	78	80	B	B	biological fallback assumption	illumina	nextseq	unknown	rrna_depletion	lexogen	bulk	bulk	bulk	Czech Republic	2021-02-17	Zygote	Embryo	Oocyte	Reproductive System
66194	66194	SRR16096233	SRX12382357	SRS10353019	SRP339082	PRJNA766854	RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos	GSE184893	Other	N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and…	pubmed:37349523	ZF zygote IP 1cell Rep5	GSM5599725	tissue:ZF zygote IP 1cell\|developmental stage:Zygote\|molecule subtype:rRNA free RNA	ZF zygote IP 1cell Rep5	Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.	ZF zygote IP 1cell	For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.	For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	developmental stage:Zygote\|molecule subtype:rRNA free RNA	GSM5599725	GSM5599725: ZF zygote IP 1cell Rep5; Danio rerio; RIP Seq	GSM5599725		1	For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	GEO Accession:GSM5599725	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP339082	loader:fastq load.py	ZF_zygote_IP_1cell_Rep5_R1.fastq.gz ZF_zygote_IP_1cell_Rep5_R2.fastq.gz	fastq fastq	3660517860.0	35887430.0	GSM5599725 r1	0:51 1:51	A:858138600;C:924733544;G:1002150083;T:875349961;N:145672	51	51	858138600	924733544	1002150083	875349961	145672	SRX12382357	SRS10353019	SRA1301707	GEO	Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan	2	0.83384	0.82667	0.09687	0.11892	0.79076	0.79326	0.63739	0.60941	51	51	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	bulk	bulk	United States	2021-09-28	Zygote	Embryo	Oocyte	Reproductive System
66195	66195	SRR16096232	SRX12382356	SRS10353018	SRP339082	PRJNA766854	RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos	GSE184893	Other	N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and…	pubmed:37349523	ZF zygote IP 1cell Rep4	GSM5599724	tissue:ZF zygote IP 1cell\|developmental stage:Zygote\|molecule subtype:rRNA free RNA	ZF zygote IP 1cell Rep4	Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.	ZF zygote IP 1cell	For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.	For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	developmental stage:Zygote\|molecule subtype:rRNA free RNA	GSM5599724	GSM5599724: ZF zygote IP 1cell Rep4; Danio rerio; RIP Seq	GSM5599724		1	For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	GEO Accession:GSM5599724	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP339082	loader:fastq load.py	ZF_zygote_IP_1cell_Rep4_R1.fastq.gz ZF_zygote_IP_1cell_Rep4_R2.fastq.gz	fastq fastq	3660205842.0	35884371.0	GSM5599724 r1	0:51 1:51	A:895738659;C:880838836;G:971118499;T:912364119;N:145729	51	51	895738659	880838836	971118499	912364119	145729	SRX12382356	SRS10353018	SRA1301707	GEO	Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan	2	0.87258	0.86932	0.06573	0.07958	0.78044	0.78374	0.55531	0.5462	51	51	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	bulk	bulk	United States	2021-09-28	Zygote	Embryo	Oocyte	Reproductive System
66196	66196	SRR16096231	SRX12382355	SRS10353016	SRP339082	PRJNA766854	RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos	GSE184893	Other	N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and…	pubmed:37349523	ZF zygote IP 1cell Rep3	GSM5599723	tissue:ZF zygote IP 1cell\|developmental stage:Zygote\|molecule subtype:rRNA free RNA	ZF zygote IP 1cell Rep3	Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.	ZF zygote IP 1cell	For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.	For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	developmental stage:Zygote\|molecule subtype:rRNA free RNA	GSM5599723	GSM5599723: ZF zygote IP 1cell Rep3; Danio rerio; RIP Seq	GSM5599723		1	For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	GEO Accession:GSM5599723	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP339082	loader:fastq load.py	ZF_zygote_IP_1cell_Rep3_R1.fastq.gz ZF_zygote_IP_1cell_Rep3_R2.fastq.gz	fastq fastq	2732409048.0	26788324.0	GSM5599723 r1	0:51 1:51	A:669345195;C:656715671;G:724415204;T:681825149;N:107829	51	51	669345195	656715671	724415204	681825149	107829	SRX12382355	SRS10353016	SRA1301707	GEO	Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan	2	0.85204	0.83607	0.06526	0.08046	0.78535	0.78748	0.60467	0.50165	51	51	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	bulk	bulk	United States	2021-09-28	Zygote	Embryo	Oocyte	Reproductive System
66197	66197	SRR16096230	SRX12382354	SRS10353017	SRP339082	PRJNA766854	RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos	GSE184893	Other	N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and…	pubmed:37349523	ZF zygote IP 1cell Rep2	GSM5599722	tissue:ZF zygote IP 1cell\|developmental stage:Zygote\|molecule subtype:rRNA free RNA	ZF zygote IP 1cell Rep2	Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.	ZF zygote IP 1cell	For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.	For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	developmental stage:Zygote\|molecule subtype:rRNA free RNA	GSM5599722	GSM5599722: ZF zygote IP 1cell Rep2; Danio rerio; RIP Seq	GSM5599722		1	For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	GEO Accession:GSM5599722	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP339082	loader:fastq load.py	ZF_zygote_IP_1cell_Rep2_R1.fastq.gz ZF_zygote_IP_1cell_Rep2_R2.fastq.gz	fastq fastq	2235668028.0	21918314.0	GSM5599722 r1	0:51 1:51	A:552522700;C:535947981;G:588168855;T:558939713;N:88779	51	51	552522700	535947981	588168855	558939713	88779	SRX12382354	SRS10353017	SRA1301707	GEO	Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan	2	0.85597	0.85298	0.06663	0.07927	0.79058	0.79237	0.57626	0.56525	51	51	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	bulk	bulk	United States	2021-09-28	Zygote	Embryo	Oocyte	Reproductive System
66198	66198	SRR16096229	SRX12382353	SRS10353015	SRP339082	PRJNA766854	RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos	GSE184893	Other	N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and…	pubmed:37349523	ZF zygote IP 1cell Rep1	GSM5599721	tissue:ZF zygote IP 1cell\|developmental stage:Zygote\|molecule subtype:rRNA free RNA	ZF zygote IP 1cell Rep1	Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.	ZF zygote IP 1cell	For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.	For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	developmental stage:Zygote\|molecule subtype:rRNA free RNA	GSM5599721	GSM5599721: ZF zygote IP 1cell Rep1; Danio rerio; RIP Seq	GSM5599721		1	For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	GEO Accession:GSM5599721	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP339082	loader:fastq load.py	ZF_zygote_IP_1cell_Rep1_R1.fastq.gz ZF_zygote_IP_1cell_Rep1_R2.fastq.gz	fastq fastq	1785761736.0	17507468.0	GSM5599721 r1	0:51 1:51	A:429081683;C:435813601;G:481376346;T:439419714;N:70392	51	51	429081683	435813601	481376346	439419714	70392	SRX12382353	SRS10353015	SRA1301707	GEO	Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan	2	0.75314	0.75693	0.0543	0.06639	0.79482	0.79594	0.57979	0.56522	51	51	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	bulk	bulk	United States	2021-09-28	Zygote	Embryo	Oocyte	Reproductive System
66199	66199	SRR16096228	SRX12382352	SRS10353014	SRP339082	PRJNA766854	RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos	GSE184893	Other	N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and…	pubmed:37349523	ZF zygote IP 5cell Rep3	GSM5599720	tissue:ZF zygote IP 5cell\|developmental stage:Zygote\|molecule subtype:rRNA free RNA	ZF zygote IP 5cell Rep3	Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.	ZF zygote IP 5cell	For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.	For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	developmental stage:Zygote\|molecule subtype:rRNA free RNA	GSM5599720	GSM5599720: ZF zygote IP 5cell Rep3; Danio rerio; RIP Seq	GSM5599720		1	For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	GEO Accession:GSM5599720	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP339082	loader:fastq load.py	ZF_zygote_IP_5cell_Rep3_R1.fastq.gz ZF_zygote_IP_5cell_Rep3_R2.fastq.gz	fastq fastq	2179659420.0	21369210.0	GSM5599720 r1	0:51 1:51	A:539092949;C:513857324;G:569620218;T:556940661;N:148268	51	51	539092949	513857324	569620218	556940661	148268	SRX12382352	SRS10353014	SRA1301707	GEO	Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan	2	0.92028	0.90706	0.03967	0.05572	0.78431	0.78886	0.49727	0.48541	51	51	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	bulk	bulk	United States	2021-09-28	Zygote	Embryo	Oocyte	Reproductive System
66200	66200	SRR16096227	SRX12382351	SRS10353012	SRP339082	PRJNA766854	RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos	GSE184893	Other	N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and…	pubmed:37349523	ZF zygote IP 5cell Rep2	GSM5599719	tissue:ZF zygote IP 5cell\|developmental stage:Zygote\|molecule subtype:rRNA free RNA	ZF zygote IP 5cell Rep2	Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.	ZF zygote IP 5cell	For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.	For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	developmental stage:Zygote\|molecule subtype:rRNA free RNA	GSM5599719	GSM5599719: ZF zygote IP 5cell Rep2; Danio rerio; RIP Seq	GSM5599719		1	For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	GEO Accession:GSM5599719	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP339082	loader:fastq load.py	ZF_zygote_IP_5cell_Rep2_R1.fastq.gz ZF_zygote_IP_5cell_Rep2_R2.fastq.gz	fastq fastq	2527184538.0	24776319.0	GSM5599719 r1	0:51 1:51	A:628307375;C:594702688;G:657847712;T:646151885;N:174878	51	51	628307375	594702688	657847712	646151885	174878	SRX12382351	SRS10353012	SRA1301707	GEO	Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan	2	0.91811	0.90487	0.03919	0.05376	0.78315	0.78729	0.49414	0.48564	51	51	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	bulk	bulk	United States	2021-09-28	Zygote	Embryo	Oocyte	Reproductive System
66201	66201	SRR16096226	SRX12382350	SRS10353011	SRP339082	PRJNA766854	RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos	GSE184893	Other	N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and…	pubmed:37349523	ZF zygote IP 5cell Rep1	GSM5599718	tissue:ZF zygote IP 5cell\|developmental stage:Zygote\|molecule subtype:rRNA free RNA	ZF zygote IP 5cell Rep1	Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.	ZF zygote IP 5cell	For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.	For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	developmental stage:Zygote\|molecule subtype:rRNA free RNA	GSM5599718	GSM5599718: ZF zygote IP 5cell Rep1; Danio rerio; RIP Seq	GSM5599718		1	For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	GEO Accession:GSM5599718	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP339082	loader:fastq load.py	ZF_zygote_IP_5cell_Rep1_R1.fastq.gz ZF_zygote_IP_5cell_Rep1_R2.fastq.gz	fastq fastq	3481342518.0	34130809.0	GSM5599718 r1	0:51 1:51	A:865680250;C:823420389;G:907146965;T:884854199;N:240715	51	51	865680250	823420389	907146965	884854199	240715	SRX12382350	SRS10353011	SRA1301707	GEO	Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan	2	0.91893	0.90939	0.04544	0.06005	0.78025	0.78348	0.50569	0.49155	51	51	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	bulk	bulk	United States	2021-09-28	Zygote	Embryo	Oocyte	Reproductive System
66202	66202	SRR16096225	SRX12382349	SRS10353013	SRP339082	PRJNA766854	RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos	GSE184893	Other	N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and…	pubmed:37349523	ZF zygote IP 10cell Rep3	GSM5599717	tissue:ZF zygote IP 10cell\|developmental stage:Zygote\|molecule subtype:rRNA free RNA	ZF zygote IP 10cell Rep3	Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.	ZF zygote IP 10cell	For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.	For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	developmental stage:Zygote\|molecule subtype:rRNA free RNA	GSM5599717	GSM5599717: ZF zygote IP 10cell Rep3; Danio rerio; RIP Seq	GSM5599717		1	For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	GEO Accession:GSM5599717	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP339082	loader:fastq load.py	ZF_zygote_IP_10cell_Rep3_R1.fastq.gz ZF_zygote_IP_10cell_Rep3_R2.fastq.gz	fastq fastq	2172362850.0	21297675.0	GSM5599717 r1	0:51 1:51	A:536043605;C:513512883;G:568368414;T:554284996;N:152952	51	51	536043605	513512883	568368414	554284996	152952	SRX12382349	SRS10353013	SRA1301707	GEO	Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan	2	0.91859	0.90522	0.03736	0.05214	0.78715	0.79129	0.49736	0.48681	51	51	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	bulk	bulk	United States	2021-09-28	Zygote	Embryo	Oocyte	Reproductive System
66203	66203	SRR16096224	SRX12382348	SRS10353010	SRP339082	PRJNA766854	RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos	GSE184893	Other	N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and…	pubmed:37349523	ZF zygote IP 10cell Rep2	GSM5599716	tissue:ZF zygote IP 10cell\|developmental stage:Zygote\|molecule subtype:rRNA free RNA	ZF zygote IP 10cell Rep2	Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.	ZF zygote IP 10cell	For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.	For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	developmental stage:Zygote\|molecule subtype:rRNA free RNA	GSM5599716	GSM5599716: ZF zygote IP 10cell Rep2; Danio rerio; RIP Seq	GSM5599716		1	For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	GEO Accession:GSM5599716	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP339082	loader:fastq load.py	ZF_zygote_IP_10cell_Rep2_R1.fastq.gz ZF_zygote_IP_10cell_Rep2_R2.fastq.gz	fastq fastq	1840839492.0	18047446.0	GSM5599716 r1	0:51 1:51	A:454385290;C:437082102;G:482351138;T:466893642;N:127320	51	51	454385290	437082102	482351138	466893642	127320	SRX12382348	SRS10353010	SRA1301707	GEO	Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan	2	0.92217	0.90956	0.04012	0.05483	0.78819	0.79318	0.49756	0.48256	51	51	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	bulk	bulk	United States	2021-09-28	Zygote	Embryo	Oocyte	Reproductive System
66204	66204	SRR16096223	SRX12382347	SRS10353009	SRP339082	PRJNA766854	RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos	GSE184893	Other	N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and…	pubmed:37349523	ZF zygote IP 10cell Rep1	GSM5599715	tissue:ZF zygote IP 10cell\|developmental stage:Zygote\|molecule subtype:rRNA free RNA	ZF zygote IP 10cell Rep1	Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.	ZF zygote IP 10cell	For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.	For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	developmental stage:Zygote\|molecule subtype:rRNA free RNA	GSM5599715	GSM5599715: ZF zygote IP 10cell Rep1; Danio rerio; RIP Seq	GSM5599715		1	For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	GEO Accession:GSM5599715	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP339082	loader:fastq load.py	ZF_zygote_IP_10cell_Rep1_R1.fastq.gz ZF_zygote_IP_10cell_Rep1_R2.fastq.gz	fastq fastq	2400553680.0	23534840.0	GSM5599715 r1	0:51 1:51	A:594878203;C:567573525;G:625488388;T:612448386;N:165178	51	51	594878203	567573525	625488388	612448386	165178	SRX12382347	SRS10353009	SRA1301707	GEO	Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan	2	0.91641	0.908	0.03979	0.05394	0.78455	0.7892	0.48862	0.47478	51	51	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	bulk	bulk	United States	2021-09-28	Zygote	Embryo	Oocyte	Reproductive System
66205	66205	SRR16096222	SRX12382346	SRS10353008	SRP339082	PRJNA766854	RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos	GSE184893	Other	N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and…	pubmed:37349523	ZF zygote Input 10cell Rep2	GSM5599714	tissue:ZF zygote Input 10cell\|developmental stage:Zygote\|molecule subtype:rRNA free RNA	ZF zygote Input 10cell Rep2	Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.	ZF zygote Input 10cell	For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.	For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	developmental stage:Zygote\|molecule subtype:rRNA free RNA	GSM5599714	GSM5599714: ZF zygote Input 10cell Rep2; Danio rerio; RIP Seq	GSM5599714		1	For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	GEO Accession:GSM5599714	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP339082	loader:fastq load.py	ZF_zygote_Input_10cell_Rep2_R1.fastq.gz ZF_zygote_Input_10cell_Rep2_R2.fastq.gz	fastq fastq	3842772582.0	37674241.0	GSM5599714 r1	0:51 1:51	A:843564828;C:1054412690;G:1130769812;T:813758353;N:266899	51	51	843564828	1054412690	1130769812	813758353	266899	SRX12382346	SRS10353008	SRA1301707	GEO	Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan	2	0.91511	0.90868	0.32791	0.38048	0.89457	0.89441	0.81532	0.75274	51	51	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	bulk	bulk	United States	2021-09-28	Zygote	Embryo	Oocyte	Reproductive System
66206	66206	SRR16096221	SRX12382345	SRS10353007	SRP339082	PRJNA766854	RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos	GSE184893	Other	N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and…	pubmed:37349523	ZF zygote Input 10cell Rep1	GSM5599713	tissue:ZF zygote Input 10cell\|developmental stage:Zygote\|molecule subtype:rRNA free RNA	ZF zygote Input 10cell Rep1	Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.	ZF zygote Input 10cell	For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.	For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	developmental stage:Zygote\|molecule subtype:rRNA free RNA	GSM5599713	GSM5599713: ZF zygote Input 10cell Rep1; Danio rerio; RIP Seq	GSM5599713		1	For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.	GEO Accession:GSM5599713	RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP339082	loader:fastq load.py	ZF_zygote_Input_10cell_Rep1_R1.fastq.gz ZF_zygote_Input_10cell_Rep1_R2.fastq.gz	fastq fastq	4029368016.0	39503608.0	GSM5599713 r1	0:51 1:51	A:893562237;C:1096986475;G:1180690796;T:857849967;N:278541	51	51	893562237	1096986475	1180690796	857849967	278541	SRX12382345	SRS10353007	SRA1301707	GEO	Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan	2	0.91491	0.90807	0.32799	0.37836	0.89292	0.89282	0.81006	0.73354	51	51	B	B	biological fallback assumption	illumina	novaseq_era	3prime	poly_a	nebnext	bulk	bulk	bulk	United States	2021-09-28	Zygote	Embryo	Oocyte	Reproductive System

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