RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

48 rows where experiment.library_selection = "other", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation_coarse = "Reproductive System"

✎ View and edit SQL

This data as json, CSV (advanced)

devstage_curation 7

experiment.library_strategy 4

devstage_curation_coarse 4

technology 3

tissue_curation 2

experiment.platform 2

experiment.library_layout 2

tissue_curation_coarse 1

  • Reproductive System · 48 ✖

experiment.library_source 1

  • TRANSCRIPTOMIC · 48 ✖

experiment.library_selection 1

  • other · 48 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_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 tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
7949 7949 ERR015566 ERX005931 ERS000090 ERP000263 PRJEB2208 Zebrafish gene three prime end pull down for genome annotation E-MTAB-308 Transcriptome Analysis         ZF ovary sample1 SAMEA708832 Wellcome Sanger Institute Alias:ZF ovary sample1|Description:RNA extracted from adult zebrafish ovary|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 02 26T10:44:13Z|INSDC last update:2018 03 08T15:24:37Z|INSDC status:public|SRA accession:ERS000090|Sample Name:ERS000090|Sex:female|Strain:Tuebingen|Title:Danio rerio                 Illumina Genome Analyzer II paired end sequencing; Zebrafish gene 3 prime end pull down for genome annotation E MTAB 308:Illumina Genome Analyzer II sequencing of adult Zebrafish ovary dpf three prime pull down paired end 250 to 300 bp insert Zebrafish adult ovary mRNA three prime end Zebrafish gene three prime end pull down for genome annotation 20 ug of total RNA was fragmented using RNA Fragmentation Reagent Ambion for 5 minutes at 70 C and ethanol precipitated with glycogen and LiCl. RNA was annealed to the oligo stBPM1polyT22 biotin GGCCAGTCCTGGAGTTTTTTTTTTTTTTTTTTTTTTVN and bound to streptavidin magnetic beads. post washing by pull down on a magnet the bound RNA was reverse transcribed with SuperScript II Invitrogen and a second strand synthesised with DNA polymerase I Promega and RNase H NEB. post further washing the double strand cDNA was released from the beads with BpmI NEB. The cDNA was recovered with the QIAgen PCR Purification Kit and made into a standard Illumina library following the manufacturer's protocol with a fragment size of 250 to 300 bp. Experimental Factor: DEVELOPMENTAL STAGE:adult|Experimental Factor: ORGANISM PART:ovary|Experimental Factor: SEX:female RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina Genome Analyzer II   ERP000263 Illumina Genome Analyzer II paired end sequencing; Zebrafish gene three prime end pull down for genome annotation ENA FIRST PUBLIC:2010 08 19|ENA LAST UPDATE:2018 11 16 3444_6.srf srf 1150193272.0 7567061.0 E MTAB 308:Illumina Genome Analyzer II sequencing of adult Zebrafish ovary dpf three prime pull down paired end 250 to 300 bp insert 0:76 1:76 A:280621121;C:291623460;G:285422205;T:273609496;N:18916990 76 76     280621121 291623460 285422205 273609496 18916990 ERX005931 ERS000090 ERA010603 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.96663 0.96605 0.0126 0.01249 0.82272 0.82548 0.45602 0.45286 76 76 B B biological fallback assumption illumina early_illumina 3prime other unknown bulk unknown unknown   United Kingdom 2010-02-26 Adult Adult Gonad Reproductive System
36285 36285 SRR363985 SRX105298 SRS270141 SRP009275 PRJNA148581 Hen1 analysis in zebrafish GSE33582 Transcriptome Analysis small RNA libraries from wild type and Hen1 mutant testes were made with either polyA tailing VASAGFPHen1minus/plus or adapter ligation Hen1Testis and WTTestis and sequenced on an Illumina GAII platform. Overall design: RNA was isolated from total testis tissue of both Hen1 wildtype and Hen1 mutant animals. post size selection from gel the small RNA libraries wre made.   pubmed:20859253   wildtype ligation GSM830247   source name:testis|strain:TL|genotype/variation:Hen1 wildtype|tissue:testis|small rna library prep method:adapter ligation wildtype ligation three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the zebrafish genome Zv8 testis   Small RNAs in the size range of 19 31 bases were excised from a denaturing gel. Adaptors were ligated to the five prime and three prime ends of the isolated RNA and the product was converted to cDNA using a primer on the three prime adaptor. post 15 cycles PCR amplification of the library the product was gel purified and sequenced on a Solexa platform.   strain:TL|genotype/variation:Hen1 wildtype|tissue:testis|small rna library prep method:adapter ligation GSM830247 GSM830247: wildtype ligation GSM830247: wildtype ligation GSM830247: wildtype ligation 1   GEO Accession:GSM830247 RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>46</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP009275   read name barcode proc directive:ignore WTTESTIS.fastq fastq 395791130.0 8604155.0 GSM830247 1 0:46 A:79045664;C:90489917;G:99082007;T:127024229;N:149313 46       79045664 90489917 99082007 127024229 149313 SRX105298 SRS270141 SRA047996 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.00021   0.00015   0.99989   0.0   46   T   under 1.2% mapping rate illumina early_illumina 5prime poly_a unknown bulk unknown unknown   Netherlands 2011-11-09 Undetermined Undetermined Gonad Reproductive System
36286 36286 SRR363984 SRX105297 SRS270140 SRP009275 PRJNA148581 Hen1 analysis in zebrafish GSE33582 Transcriptome Analysis small RNA libraries from wild type and Hen1 mutant testes were made with either polyA tailing VASAGFPHen1minus/plus or adapter ligation Hen1Testis and WTTestis and sequenced on an Illumina GAII platform. Overall design: RNA was isolated from total testis tissue of both Hen1 wildtype and Hen1 mutant animals. post size selection from gel the small RNA libraries wre made.   pubmed:20859253   hen1 mutant ligation GSM830246   source name:testis|strain:TL|genotype/variation:Hen1 mutant|tissue:testis|small rna library prep method:adapter ligation hen1 mutant ligation three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the zebrafish genome Zv8 testis   Small RNAs in the size range of 19 31 bases were excised from a denaturing gel. Adaptors were ligated to the five prime and three prime ends of the isolated RNA and the product was converted to cDNA using a primer on the three prime adaptor. post 15 cycles PCR amplification of the library the product was gel purified and sequenced on a Solexa platform.   strain:TL|genotype/variation:Hen1 mutant|tissue:testis|small rna library prep method:adapter ligation GSM830246 GSM830246: hen1 mutant ligation GSM830246: hen1 mutant ligation GSM830246: hen1 mutant ligation 1   GEO Accession:GSM830246 RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>46</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP009275   read name barcode proc directive:ignore HEN1TESTIS.fastq fastq 440876374.0 9584269.0 GSM830246 1 0:46 A:91693980;C:99515953;G:105634029;T:143841954;N:190458 46       91693980 99515953 105634029 143841954 190458 SRX105297 SRS270140 SRA047996 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.00039   0.00033   0.99995   0.0   46   T   under 1.2% mapping rate illumina early_illumina 5prime poly_a unknown bulk unknown unknown   Netherlands 2011-11-09 Undetermined Undetermined Gonad Reproductive System
36287 36287 SRR363983 SRX105296 SRS270139 SRP009275 PRJNA148581 Hen1 analysis in zebrafish GSE33582 Transcriptome Analysis small RNA libraries from wild type and Hen1 mutant testes were made with either polyA tailing VASAGFPHen1minus/plus or adapter ligation Hen1Testis and WTTestis and sequenced on an Illumina GAII platform. Overall design: RNA was isolated from total testis tissue of both Hen1 wildtype and Hen1 mutant animals. post size selection from gel the small RNA libraries wre made.   pubmed:20859253   wildtype polyA GSM830245   source name:testis|strain:TL|genotype/variation:Hen1 wildtype|tissue:testis|small rna library prep method:polyA tailing wildtype polyA three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the zebrafish genome Zv8 testis   Small RNAs in the size range of 19 31 bases were excised from a denaturing gel. RNA was polyA tailed using polyA polymerase followed by ligation of a RNA adaptor to the five prime phosphate of the small RNAs. First strand cDNA synthesis was performed using an oligodT linker primer and M MLV RNase H reverse transcriptase. post amplification the cDNA was sent for sequencing on an Illumina/Solexa platform.   strain:TL|genotype/variation:Hen1 wildtype|tissue:testis|small rna library prep method:polyA tailing GSM830245 GSM830245: wildtype polyA GSM830245: wildtype polyA GSM830245: wildtype polyA 1   GEO Accession:GSM830245 RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>44</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP009275   read name barcode proc directive:ignore VASAGFPHEN1plusMALE.fastq fastq 167344144.0 3803276.0 GSM830245 1 0:44 A:87935982;C:21182538;G:19081938;T:34474815;N:4668871 44       87935982 21182538 19081938 34474815 4668871 SRX105296 SRS270139 SRA047996 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.06642   0.05042   0.99226   0.38346   44   B   usable mapping rate illumina early_illumina unknown poly_a unknown bulk unknown unknown   Netherlands 2011-11-09 Undetermined Undetermined Gonad Reproductive System
40701 40701 SRR3231363 SRX1637111 SRS1342926 SRP071849 PRJNA315400 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq] GSE79161 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction. parent bioproject:PRJNA315403 pubmed:30086300   Input 3 GSM2087141   tissue:Zebrafish Zygotes|fraction:Input Input 3 Reads were mapped to Zv9 using tophat trapnell et al 2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al 2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name. Zebrafish Zygotes   mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing. Zebrafish were maintained under standard conditions. fraction:Input GSM2087141 GSM2087141: Input 3; Danio rerio; RIP Seq GSM2087141   1 mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing. GEO Accession:GSM2087141 RIP-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP071849     WT_Input_3.fastq.gz fastq 1902296226.0 37299926.0 GSM2087141 r1 0:51 A:466290166;C:465344039;G:486942278;T:483240280;N:479463 51       466290166 465344039 486942278 483240280 479463 SRX1637111 SRS1342926 SRA385813 GEO Rene Ketting, RNA silencing, IMB 1 0.85793   0.14814   0.79941   0.55214   51   B   usable mapping rate illumina hiseq_era unknown other unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2016-03-13 Zygote Embryo Oocyte Reproductive System
40702 40702 SRR3231362 SRX1637110 SRS1342927 SRP071849 PRJNA315400 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq] GSE79161 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction. parent bioproject:PRJNA315403 pubmed:30086300   Input 2 GSM2087140   tissue:Zebrafish Zygotes|fraction:Input Input 2 Reads were mapped to Zv9 using tophat trapnell et al 2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al 2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name. Zebrafish Zygotes   mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing. Zebrafish were maintained under standard conditions. fraction:Input GSM2087140 GSM2087140: Input 2; Danio rerio; RIP Seq GSM2087140   1 mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing. GEO Accession:GSM2087140 RIP-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP071849     WT_Input_2.fastq.gz fastq 1540737999.0 30210549.0 GSM2087140 r1 0:51 A:380481772;C:379741192;G:395453141;T:384675313;N:386581 51       380481772 379741192 395453141 384675313 386581 SRX1637110 SRS1342927 SRA385813 GEO Rene Ketting, RNA silencing, IMB 1 0.8787   0.14935   0.79202   0.54381   51   B   usable mapping rate illumina hiseq_era unknown other unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2016-03-13 Zygote Embryo Oocyte Reproductive System
40703 40703 SRR3231361 SRX1637109 SRS1342928 SRP071849 PRJNA315400 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq] GSE79161 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction. parent bioproject:PRJNA315403 pubmed:30086300   Input 1 GSM2087139   tissue:Zebrafish Zygotes|fraction:Input Input 1 Reads were mapped to Zv9 using tophat trapnell et al 2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al 2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name. Zebrafish Zygotes   mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing. Zebrafish were maintained under standard conditions. fraction:Input GSM2087139 GSM2087139: Input 1; Danio rerio; RIP Seq GSM2087139   1 mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing. GEO Accession:GSM2087139 RIP-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP071849     WT_Input_1.fastq.gz fastq 1109818905.0 21761155.0 GSM2087139 r1                       SRX1637109 SRS1342928 SRA385813 GEO Rene Ketting, RNA silencing, IMB 1 0.87467   0.18794   0.79411   0.63378   51   B   usable mapping rate illumina hiseq_era unknown other unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2016-03-13 Zygote Embryo Oocyte Reproductive System
40704 40704 SRR3231360 SRX1637108 SRS1342929 SRP071849 PRJNA315400 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq] GSE79161 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction. parent bioproject:PRJNA315403 pubmed:30086300   Tdrd6a IP 3 GSM2087138   tissue:Zebrafish Zygotes|fraction:Tdrd6a IP Tdrd6a IP 3 Reads were mapped to Zv9 using tophat trapnell et al 2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al 2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name. Zebrafish Zygotes   mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing. Zebrafish were maintained under standard conditions. fraction:Tdrd6a IP GSM2087138 GSM2087138: Tdrd6a IP 3; Danio rerio; RIP Seq GSM2087138   1 mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing. GEO Accession:GSM2087138 RIP-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP071849     WT_Tdrd6a_IP_3.fastq.gz fastq 843641439.0 16541989.0 GSM2087138 r1 0:51 A:216465581;C:196892096;G:207722567;T:222361382;N:199813 51       216465581 196892096 207722567 222361382 199813 SRX1637108 SRS1342929 SRA385813 GEO Rene Ketting, RNA silencing, IMB 1 0.84615   0.08957   0.78768   0.50612   51   B   usable mapping rate illumina hiseq_era unknown other unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2016-03-13 Zygote Embryo Oocyte Reproductive System
40705 40705 SRR3231359 SRX1637107 SRS1342930 SRP071849 PRJNA315400 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq] GSE79161 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction. parent bioproject:PRJNA315403 pubmed:30086300   Tdrd6a IP 2 GSM2087137   tissue:Zebrafish Zygotes|fraction:Tdrd6a IP Tdrd6a IP 2 Reads were mapped to Zv9 using tophat trapnell et al 2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al 2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name. Zebrafish Zygotes   mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing. Zebrafish were maintained under standard conditions. fraction:Tdrd6a IP GSM2087137 GSM2087137: Tdrd6a IP 2; Danio rerio; RIP Seq GSM2087137   1 mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing. GEO Accession:GSM2087137 RIP-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP071849     WT_Tdrd6a_IP_2.fastq.gz fastq 391198050.0 7670550.0 GSM2087137 r1 0:51 A:99015594;C:91525929;G:97155710;T:103371571;N:129246 51       99015594 91525929 97155710 103371571 129246 SRX1637107 SRS1342930 SRA385813 GEO Rene Ketting, RNA silencing, IMB 1 0.85778   0.12015   0.80515   0.47541   51   B   usable mapping rate illumina hiseq_era unknown other unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2016-03-13 Zygote Embryo Oocyte Reproductive System
40706 40706 SRR3231358 SRX1637106 SRS1342931 SRP071849 PRJNA315400 Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq] GSE79161 Transcriptome Analysis Germ plasm the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs without xxx effects on piRNA biogenesis signatures. Second we show that Tdrd6a is required for Balbiani body and germ plasm integrity and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level maternally contributed Tdrd6a strongly impacts germ cell formation but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction. parent bioproject:PRJNA315403 pubmed:30086300   Tdrd6a IP 1 GSM2087136   tissue:Zebrafish Zygotes|fraction:Tdrd6a IP Tdrd6a IP 1 Reads were mapped to Zv9 using tophat trapnell et al 2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al 2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name. Zebrafish Zygotes   mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing. Zebrafish were maintained under standard conditions. fraction:Tdrd6a IP GSM2087136 GSM2087136: Tdrd6a IP 1; Danio rerio; RIP Seq GSM2087136   1 mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing. GEO Accession:GSM2087136 RIP-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000   SRP071849     WT_Tdrd6a_IP_1.fastq.gz fastq 1927415052.0 37792452.0 GSM2087136 r1 0:51 A:498125298;C:444860381;G:468826607;T:515142356;N:460410 51       498125298 444860381 468826607 515142356 460410 SRX1637106 SRS1342931 SRA385813 GEO Rene Ketting, RNA silencing, IMB 1 0.86194   0.09753   0.80146   0.47808   51   B   usable mapping rate illumina hiseq_era unknown other unknown sc_generic single_cell_generic generic-scrnaseq-only   Germany 2016-03-13 Zygote Embryo Oocyte Reproductive System
44644 44644 SRR6268204 SRX3374372 SRS2671596 SRP124609 PRJNA417597 Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation GSE106677 Other The stability of mRNAs is regulated by signals within their sequences but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here we introduce UTR Seq a combination of massively parallel reporter assays and regression models to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment a sample was collected every hour between 1h to 8h and at 10h. In the second experiment a single sample was collected every hour between 1h to 10h and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A reporters in two separate experiments. In the first experiment a sample was collected every hour between 1h to 8h and at 10h. In the second experiment rep samples were coll…   pubmed:29225039   oocyte A+ 7h GSM2845358   source name:zebrafish oocyte|developmental stage:7h|tissue:oocyte oocyte A+ 7h Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg lowest 3.125fg and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels zebrafish oocyte Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage. Total RNA was isolated using TRIzol Invitrogen post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors Fertilized zebrafish eggs or oocytes were collected at 28C and kept in culture medium 5.03mM NaCl 0.17mM KCl 0.33mM CaCl2 0.33mM MgSo4 0.1% Methylene blue. A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage. developmental stage:7h|tissue:oocyte GSM2845358 GSM2845358: oocyte A+ 7h; Danio rerio; OTHER GSM2845358   1 Total RNA was isolated using TRIzol Invitrogen post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors GEO Accession:GSM2845358 OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina MiSeq   SRP124609     AR22-SL21.fastq.gz fastq 463495840.0 2896849.0 GSM2845358 r1 0:160 1:0 A:145685088;C:104925443;G:89232572;T:123650704;N:2033 160 0     145685088 104925443 89232572 123650704 2033 SRX3374372 SRS2671596 SRA629220 GEO Broad Institute 1 4e-05   1e-05   0.99991   0.5   160   T   under 1.2% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   United States 2017-11-08 Gastrula Embryo Oocyte Reproductive System
44645 44645 SRR6268203 SRX3374371 SRS2671594 SRP124609 PRJNA417597 Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation GSE106677 Other The stability of mRNAs is regulated by signals within their sequences but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here we introduce UTR Seq a combination of massively parallel reporter assays and regression models to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment a sample was collected every hour between 1h to 8h and at 10h. In the second experiment a single sample was collected every hour between 1h to 10h and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A reporters in two separate experiments. In the first experiment a sample was collected every hour between 1h to 8h and at 10h. In the second experiment rep samples were coll…   pubmed:29225039   oocyte A+ 4h GSM2845357   source name:zebrafish oocyte|developmental stage:4h|tissue:oocyte oocyte A+ 4h Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg lowest 3.125fg and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels zebrafish oocyte Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage. Total RNA was isolated using TRIzol Invitrogen post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors Fertilized zebrafish eggs or oocytes were collected at 28C and kept in culture medium 5.03mM NaCl 0.17mM KCl 0.33mM CaCl2 0.33mM MgSo4 0.1% Methylene blue. A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage. developmental stage:4h|tissue:oocyte GSM2845357 GSM2845357: oocyte A+ 4h; Danio rerio; OTHER GSM2845357   1 Total RNA was isolated using TRIzol Invitrogen post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors GEO Accession:GSM2845357 OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina MiSeq   SRP124609     AR21-SL41.fastq.gz fastq 474802240.0 2967514.0 GSM2845357 r1 0:160 1:0 A:145810423;C:111330144;G:93000312;T:124660574;N:787 160 0     145810423 111330144 93000312 124660574 787 SRX3374371 SRS2671594 SRA629220 GEO Broad Institute 1 2e-05   0.0   0.99997   0.0   160   T   under 1.2% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   United States 2017-11-08 Blastula Embryo Oocyte Reproductive System
44646 44646 SRR6268202 SRX3374370 SRS2671595 SRP124609 PRJNA417597 Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation GSE106677 Other The stability of mRNAs is regulated by signals within their sequences but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here we introduce UTR Seq a combination of massively parallel reporter assays and regression models to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment a sample was collected every hour between 1h to 8h and at 10h. In the second experiment a single sample was collected every hour between 1h to 10h and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A reporters in two separate experiments. In the first experiment a sample was collected every hour between 1h to 8h and at 10h. In the second experiment rep samples were coll…   pubmed:29225039   oocyte A+ 1h GSM2845356   source name:zebrafish oocyte|developmental stage:1h|tissue:oocyte oocyte A+ 1h Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg lowest 3.125fg and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels zebrafish oocyte Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage. Total RNA was isolated using TRIzol Invitrogen post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors Fertilized zebrafish eggs or oocytes were collected at 28C and kept in culture medium 5.03mM NaCl 0.17mM KCl 0.33mM CaCl2 0.33mM MgSo4 0.1% Methylene blue. A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage. developmental stage:1h|tissue:oocyte GSM2845356 GSM2845356: oocyte A+ 1h; Danio rerio; OTHER GSM2845356   1 Total RNA was isolated using TRIzol Invitrogen post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors GEO Accession:GSM2845356 OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina MiSeq   SRP124609     AR20.fastq.gz fastq 647004960.0 4043781.0 GSM2845356 r1 0:160 1:0 A:196358573;C:155899107;G:129095192;T:165649225;N:2863 160 0     196358573 155899107 129095192 165649225 2863 SRX3374370 SRS2671595 SRA629220 GEO Broad Institute 1 1e-05   0.0   0.99997   0.0   160   T   under 1.2% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   United States 2017-11-08 Cleavage Embryo Oocyte Reproductive System
44647 44647 SRR6268201 SRX3374369 SRS2671601 SRP124609 PRJNA417597 Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation GSE106677 Other The stability of mRNAs is regulated by signals within their sequences but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here we introduce UTR Seq a combination of massively parallel reporter assays and regression models to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment a sample was collected every hour between 1h to 8h and at 10h. In the second experiment a single sample was collected every hour between 1h to 10h and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A reporters in two separate experiments. In the first experiment a sample was collected every hour between 1h to 8h and at 10h. In the second experiment rep samples were coll…   pubmed:29225039   oocyte A 7h GSM2845355   source name:zebrafish oocyte|developmental stage:7h|tissue:oocyte oocyte A 7h Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg lowest 3.125fg and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels zebrafish oocyte Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage. Total RNA was isolated using TRIzol Invitrogen post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors Fertilized zebrafish eggs or oocytes were collected at 28C and kept in culture medium 5.03mM NaCl 0.17mM KCl 0.33mM CaCl2 0.33mM MgSo4 0.1% Methylene blue. A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage. developmental stage:7h|tissue:oocyte GSM2845355 GSM2845355: oocyte A 7h; Danio rerio; OTHER GSM2845355   1 Total RNA was isolated using TRIzol Invitrogen post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors GEO Accession:GSM2845355 OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina MiSeq   SRP124609     AR19-SL40.fastq.gz fastq 437084640.0 2731779.0 GSM2845355 r1 0:160 1:0 A:138575507;C:98512376;G:80808399;T:119186452;N:1906 160 0     138575507 98512376 80808399 119186452 1906 SRX3374369 SRS2671601 SRA629220 GEO Broad Institute 1 2e-05   0.0   0.99995   1.0   160   T   under 1.2% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   United States 2017-11-08 Gastrula Embryo Oocyte Reproductive System
44648 44648 SRR6268200 SRX3374368 SRS2671593 SRP124609 PRJNA417597 Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation GSE106677 Other The stability of mRNAs is regulated by signals within their sequences but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here we introduce UTR Seq a combination of massively parallel reporter assays and regression models to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment a sample was collected every hour between 1h to 8h and at 10h. In the second experiment a single sample was collected every hour between 1h to 10h and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A reporters in two separate experiments. In the first experiment a sample was collected every hour between 1h to 8h and at 10h. In the second experiment rep samples were coll…   pubmed:29225039   oocyte A 4h GSM2845354   source name:zebrafish oocyte|developmental stage:4h|tissue:oocyte oocyte A 4h Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg lowest 3.125fg and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels zebrafish oocyte Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage. Total RNA was isolated using TRIzol Invitrogen post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors Fertilized zebrafish eggs or oocytes were collected at 28C and kept in culture medium 5.03mM NaCl 0.17mM KCl 0.33mM CaCl2 0.33mM MgSo4 0.1% Methylene blue. A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage. developmental stage:4h|tissue:oocyte GSM2845354 GSM2845354: oocyte A 4h; Danio rerio; OTHER GSM2845354   1 Total RNA was isolated using TRIzol Invitrogen post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors GEO Accession:GSM2845354 OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina MiSeq   SRP124609     AR18-SL39.fastq.gz fastq 533958880.0 3337243.0 GSM2845354 r1 0:160 1:0 A:163118236;C:125487590;G:106580813;T:138769793;N:2448 160 0     163118236 125487590 106580813 138769793 2448 SRX3374368 SRS2671593 SRA629220 GEO Broad Institute 1 1e-05   0.0   0.99997   0.0   160   T   under 1.2% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   United States 2017-11-08 Blastula Embryo Oocyte Reproductive System
44649 44649 SRR6268199 SRX3374367 SRS2671602 SRP124609 PRJNA417597 Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation GSE106677 Other The stability of mRNAs is regulated by signals within their sequences but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here we introduce UTR Seq a combination of massively parallel reporter assays and regression models to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment a sample was collected every hour between 1h to 8h and at 10h. In the second experiment a single sample was collected every hour between 1h to 10h and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A reporters in two separate experiments. In the first experiment a sample was collected every hour between 1h to 8h and at 10h. In the second experiment rep samples were coll…   pubmed:29225039   oocyte A 1h GSM2845353   source name:zebrafish oocyte|developmental stage:1h|tissue:oocyte oocyte A 1h Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg lowest 3.125fg and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels zebrafish oocyte Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage. Total RNA was isolated using TRIzol Invitrogen post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors Fertilized zebrafish eggs or oocytes were collected at 28C and kept in culture medium 5.03mM NaCl 0.17mM KCl 0.33mM CaCl2 0.33mM MgSo4 0.1% Methylene blue. A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage. developmental stage:1h|tissue:oocyte GSM2845353 GSM2845353: oocyte A 1h; Danio rerio; OTHER GSM2845353   1 Total RNA was isolated using TRIzol Invitrogen post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors GEO Accession:GSM2845353 OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina MiSeq   SRP124609     AR17-SL38.fastq.gz fastq 532076160.0 3325476.0 GSM2845353 r1 0:160 1:0 A:162057480;C:125858627;G:108494717;T:135663057;N:2279 160 0     162057480 125858627 108494717 135663057 2279 SRX3374367 SRS2671602 SRA629220 GEO Broad Institute 1 2e-05   0.0   0.99995   1.0   160   T   under 1.2% mapping rate illumina miseq unknown random_priming unknown bulk unknown unknown   United States 2017-11-08 Cleavage Embryo Oocyte Reproductive System
59512 59512 SRR11924307 SRX8469983 SRS6770634 SRP265951 PRJNA637293 The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites GSE151797 Other A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.   pubmed:32912962   Unf egg 3 GSM4591051   source name:unfertilized egg|tissue:unfertilized egg|rna fraction:size fractionated 20 40 nt whole cell RNA Unf egg 3 Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence. unfertilized egg   Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description   tissue:unfertilized egg|rna fraction:size fractionated 20 40 nt whole cell RNA GSM4591051 GSM4591051: Unf egg 3; Danio rerio; OTHER GSM4591051   1 Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description GEO Accession:GSM4591051 OTHER TRANSCRIPTOMIC other SINGLE ION_TORRENT Ion Torrent Proton   SRP265951   intentional duplicate GSE151797_Reference_sequence.fa Unf_egg_3.bam bam bam 149835556.0 5777340.0 GSM4591051 r1 0:25.94 A:27873539;C:50837956;G:37710769;T:33413292;N:0 25       27873539 50837956 37710769 33413292 0 SRX8469983 SRS6770634 SRA1083099 GEO RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen 1 0.74561   0.22616   0.89441   0.76897   34   B   usable mapping rate ion_torrent ion_torrent 5prime small_rna unknown bulk unknown unknown   Denmark 2020-06-04 Zygote Embryo Oocyte Reproductive System
59513 59513 SRR11924305 SRX8469982 SRS6770633 SRP265951 PRJNA637293 The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites GSE151797 Other A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.   pubmed:32912962   Unf egg 2 GSM4591050   source name:unfertilized egg|tissue:unfertilized egg|rna fraction:size fractionated 20 40 nt whole cell RNA Unf egg 2 Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence. unfertilized egg   Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description   tissue:unfertilized egg|rna fraction:size fractionated 20 40 nt whole cell RNA GSM4591050 GSM4591050: Unf egg 2; Danio rerio; OTHER GSM4591050   1 Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description GEO Accession:GSM4591050 OTHER TRANSCRIPTOMIC other SINGLE ION_TORRENT Ion Torrent Proton   SRP265951   intentional duplicate GSE151797_Reference_sequence.fa Unf_egg_2.bam bam bam 235014832.0 8915586.0 GSM4591050 r1 0:26.36 A:43825969;C:79775479;G:60531219;T:50882165;N:0 26       43825969 79775479 60531219 50882165 0 SRX8469982 SRS6770633 SRA1083099 GEO RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen 1 0.78414   0.23044   0.90352   0.76934   40   B   usable mapping rate ion_torrent ion_torrent 5prime small_rna unknown bulk unknown unknown   Denmark 2020-06-04 Zygote Embryo Oocyte Reproductive System
59514 59514 SRR11924304 SRX8469981 SRS6770632 SRP265951 PRJNA637293 The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites GSE151797 Other A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.   pubmed:32912962   Unf egg 1 GSM4591049   source name:unfertilized egg|tissue:unfertilized egg|rna fraction:size fractionated 20 40 nt whole cell RNA Unf egg 1 Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence. unfertilized egg   Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description   tissue:unfertilized egg|rna fraction:size fractionated 20 40 nt whole cell RNA GSM4591049 GSM4591049: Unf egg 1; Danio rerio; OTHER GSM4591049   1 Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description GEO Accession:GSM4591049 OTHER TRANSCRIPTOMIC other SINGLE ION_TORRENT Ion Torrent Proton   SRP265951   intentional duplicate GSE151797_Reference_sequence.fa Unf_egg_1.bam bam bam 245529952.0 9182415.0 GSM4591049 r1 0:26.74 A:46557080;C:80893860;G:66050448;T:52028564;N:0 26       46557080 80893860 66050448 52028564 0 SRX8469981 SRS6770632 SRA1083099 GEO RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen 1 0.87423   0.27943   0.91721   0.76816   37   B   usable mapping rate ion_torrent ion_torrent 5prime small_rna unknown bulk unknown unknown   Denmark 2020-06-04 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
68053 68053 SRR17592787 SRX13761632 SRS11641838 SRP354757 PRJNA796639 Augmentation of progestin signaling rescues testis organization and spermatogenesis in zebrafish with the depletion of androgen signaling PRJNA796639 Other         Tko tko   strain:AB tko|age:6 month|dev stage:adult|sex:male|tissue:gonad|BioSampleModel:Model organism or animal                 adult male gonad tko cyp17a1 / ;ar / ;npgr / gonad     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP354757     tko_R1.fastq.gz tko_R2.fastq.gz fastq fastq 6433498200.0 21444994.0 tko R1.fastq.gz 0:150 1:150 A:1734295551;C:1481922056;G:1500397917;T:1716815178;N:67498 150 150     1734295551 1481922056 1500397917 1716815178 67498 SRX13761632 SRS11641838 SRA1356016 Chinese Academy of Sciences|Institute of Hydrology Chinese Academy of Sciences 2 0.92657 0.92706 0.08532 0.08571 0.6225 0.62467 0.48954 0.48644 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2022-01-12 Adult Adult Gonad Reproductive System
68054 68054 SRR17592788 SRX13761631 SRS11641837 SRP354757 PRJNA796639 Augmentation of progestin signaling rescues testis organization and spermatogenesis in zebrafish with the depletion of androgen signaling PRJNA796639 Other         Ar apdko   strain:AB apdko|age:6 month|dev stage:adult|sex:male|tissue:gonad|BioSampleModel:Model organism or animal                 adult male gonad apdko ar / ;npgr / gonad     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP354757     apdko_R1.fastq.gz apdko_R2.fastq.gz fastq fastq 6641915400.0 22139718.0 apdko R1.fastq.gz 0:150 1:150 A:1791028372;C:1527238557;G:1556140309;T:1767435695;N:72467 150 150     1791028372 1527238557 1556140309 1767435695 72467 SRX13761631 SRS11641837 SRA1356016 Chinese Academy of Sciences|Institute of Hydrology Chinese Academy of Sciences 2 0.92557 0.92557 0.09181 0.09106 0.60229 0.60405 0.49189 0.49194 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2022-01-12 Adult Adult Gonad Reproductive System
68055 68055 SRR17592789 SRX13761630 SRS11641836 SRP354757 PRJNA796639 Augmentation of progestin signaling rescues testis organization and spermatogenesis in zebrafish with the depletion of androgen signaling PRJNA796639 Other         Cpdko cpdko   strain:AB cpdko|age:6 month|dev stage:adult|sex:male|tissue:gonad|BioSampleModel:Model organism or animal                 adult male gonad cpdko cyp17a1 / ;npgr / gonad     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP354757     cpdko_R1.fastq.gz cpdko_R2.fastq.gz fastq fastq 6099098100.0 20330327.0 cpdko R1.fastq.gz 0:150 1:150 A:1650048704;C:1398765282;G:1417954594;T:1632265804;N:63716 150 150     1650048704 1398765282 1417954594 1632265804 63716 SRX13761630 SRS11641836 SRA1356016 Chinese Academy of Sciences|Institute of Hydrology Chinese Academy of Sciences 2 0.92523 0.92507 0.08964 0.08886 0.63092 0.63238 0.48939 0.48876 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2022-01-12 Adult Adult Gonad Reproductive System
68056 68056 SRR17592790 SRX13761629 SRS11641835 SRP354757 PRJNA796639 Augmentation of progestin signaling rescues testis organization and spermatogenesis in zebrafish with the depletion of androgen signaling PRJNA796639 Other         Cadko cadko   strain:AB cadko|age:6 month|dev stage:adult|sex:male|tissue:gonad|BioSampleModel:Model organism or animal                 adult male gonad cadko cyp17a1 / ;ar / gonad     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP354757     cadko_R1.fastq.gz cadko_R2.fastq.gz fastq fastq 6438923700.0 21463079.0 cadko R1.fastq.gz 0:150 1:150 A:1742816670;C:1475435736;G:1495816081;T:1724787429;N:67784 150 150     1742816670 1475435736 1495816081 1724787429 67784 SRX13761629 SRS11641835 SRA1356016 Chinese Academy of Sciences|Institute of Hydrology Chinese Academy of Sciences 2 0.92668 0.92686 0.09755 0.09752 0.6244 0.6244 0.48164 0.48301 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2022-01-12 Adult Adult Gonad Reproductive System
68057 68057 SRR17592791 SRX13761628 SRS11641834 SRP354757 PRJNA796639 Augmentation of progestin signaling rescues testis organization and spermatogenesis in zebrafish with the depletion of androgen signaling PRJNA796639 Other         Npgr npgr   strain:AB npgr|age:6 month|dev stage:adult|sex:male|tissue:gonad|BioSampleModel:Model organism or animal                 adult male gonad npgr npgr / gonad     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP354757     npgr_R1.fastq.gz npgr_R2.fastq.gz fastq fastq 6085577700.0 20285259.0 npgr R1.fastq.gz 0:150 1:150 A:1636849675;C:1404433783;G:1424043443;T:1620187148;N:63651 150 150     1636849675 1404433783 1424043443 1620187148 63651 SRX13761628 SRS11641834 SRA1356016 Chinese Academy of Sciences|Institute of Hydrology Chinese Academy of Sciences 2 0.93185 0.93113 0.08334 0.08306 0.63536 0.6354 0.47709 0.48303 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2022-01-12 Adult Adult Gonad Reproductive System
68058 68058 SRR17592792 SRX13761627 SRS11641839 SRP354757 PRJNA796639 Augmentation of progestin signaling rescues testis organization and spermatogenesis in zebrafish with the depletion of androgen signaling PRJNA796639 Other         Ar ar   strain:AB ar|age:6 month|dev stage:adult|sex:male|tissue:gonad|BioSampleModel:Model organism or animal                 adult male gonad ar ar / gonad     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP354757     ar_R1.fastq.gz ar_R2.fastq.gz fastq fastq 6301409100.0 21004697.0 ar R1.fastq.gz 0:150 1:150 A:1708779082;C:1441426253;G:1457021310;T:1694116414;N:66041 150 150     1708779082 1441426253 1457021310 1694116414 66041 SRX13761627 SRS11641839 SRA1356016 Chinese Academy of Sciences|Institute of Hydrology Chinese Academy of Sciences 2 0.91854 0.91827 0.0948 0.09519 0.60825 0.60898 0.48564 0.48649 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2022-01-12 Adult Adult Gonad Reproductive System
68059 68059 SRR17592793 SRX13761626 SRS11641833 SRP354757 PRJNA796639 Augmentation of progestin signaling rescues testis organization and spermatogenesis in zebrafish with the depletion of androgen signaling PRJNA796639 Other         Cyp17a cyp17a   strain:AB Cyp17a|age:6 month|dev stage:adult|sex:male|tissue:gonad|BioSampleModel:Model organism or animal                 adult male gonad cyp17a cyp17a1 / gonad     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP354757     cyp17a_R1.fastq.gz cyp17a_R2.fastq.gz fastq fastq 6352758900.0 21175863.0 cyp17a R1.fastq.gz 0:150 1:150 A:1715535098;C:1458777520;G:1479671763;T:1698708117;N:66402 150 150     1715535098 1458777520 1479671763 1698708117 66402 SRX13761626 SRS11641833 SRA1356016 Chinese Academy of Sciences|Institute of Hydrology Chinese Academy of Sciences 2 0.92976 0.92823 0.0895 0.08895 0.63078 0.63236 0.49051 0.48397 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2022-01-12 Adult Adult Gonad Reproductive System
68060 68060 SRR17592794 SRX13761625 SRS11641832 SRP354757 PRJNA796639 Augmentation of progestin signaling rescues testis organization and spermatogenesis in zebrafish with the depletion of androgen signaling PRJNA796639 Other         Con con   strain:AB WT|age:6 month|dev stage:adult|sex:male|tissue:gonad|BioSampleModel:Model organism or animal                 adult male gonad con control gonad     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 4000   SRP354757     con_R1.fastq.gz con_R2.fastq.gz fastq fastq 6451282800.0 21504276.0 con R1.fastq.gz 0:150 1:150 A:1739038433;C:1485578155;G:1502949152;T:1723649684;N:67376 150 150     1739038433 1485578155 1502949152 1723649684 67376 SRX13761625 SRS11641832 SRA1356016 Chinese Academy of Sciences|Institute of Hydrology Chinese Academy of Sciences 2 0.92909 0.92982 0.08557 0.08607 0.63453 0.637 0.48821 0.48843 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2022-01-12 Adult Adult Gonad Reproductive System
68556 68556 SRR18028171 SRX14182301 SRS12005942 SRP359829 PRJNA807002 samll RNA seq of zebrafish gonads of wildtype and pld6 / at 22 dpf PRJNA807002 Other In this study we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 / gonad with three repetition. In pld6 / gonad small RNAs mapped to the known piRNA clusters were almost absent. Moreover piRNA clusters in pld6 / gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.         6WT 3   strain:AB|isolate:replicate3|ecotype:wt|age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal                 wt 3 S11 L001 R1 011 011 Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat and three repeats were performed for samll RNA sequencing.     ncRNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA HiSeq X Ten   SRP359829     wt-3_S11_L001_R1_001.fastq.gz wt-3_S11_L001_R2_001.fastq.gz fastq fastq 3576981600.0 11923272.0 wt 3 S11 L001 R1 001.fastq.gz 0:150 1:150 A:689001630;C:496844981;G:1779990511;T:610974133;N:170345 150 150     689001630 496844981 1779990511 610974133 170345 SRX14182301 SRS12005942 SRA1372890 Huazhong agricultural university|School of Life Science and Technology Huazhong agricultural university 2 0.8179 0.81697 0.60905 0.60864 0.82692 0.82915 0.52425 0.52623 150 150 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   China 2022-02-14 Multi-stage Multi-stage Gonad Reproductive System
68557 68557 SRR18028172 SRX14182300 SRS12005941 SRP359829 PRJNA807002 samll RNA seq of zebrafish gonads of wildtype and pld6 / at 22 dpf PRJNA807002 Other In this study we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 / gonad with three repetition. In pld6 / gonad small RNAs mapped to the known piRNA clusters were almost absent. Moreover piRNA clusters in pld6 / gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.         5WT 2   strain:AB|isolate:replicate2|ecotype:wt|age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal                 wt 2 S10 L001 R1 009 009 Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat and three repeats were performed for samll RNA sequencing.     ncRNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA HiSeq X Ten   SRP359829     wt-2_S10_L001_R1_001.fastq.gz wt-2_S10_L001_R2_001.fastq.gz fastq fastq 4200013800.0 14000046.0 wt 2 S10 L001 R1 001.fastq.gz 0:150 1:150 A:781057232;C:617020885;G:2110010128;T:691723797;N:201758 150 150     781057232 617020885 2110010128 691723797 201758 SRX14182300 SRS12005941 SRA1372890 Huazhong agricultural university|School of Life Science and Technology Huazhong agricultural university 2 0.8213 0.82216 0.59414 0.59507 0.81089 0.81306 0.53839 0.52755 150 150 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   China 2022-02-14 Multi-stage Multi-stage Gonad Reproductive System
68558 68558 SRR18028173 SRX14182299 SRS12005940 SRP359829 PRJNA807002 samll RNA seq of zebrafish gonads of wildtype and pld6 / at 22 dpf PRJNA807002 Other In this study we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 / gonad with three repetition. In pld6 / gonad small RNAs mapped to the known piRNA clusters were almost absent. Moreover piRNA clusters in pld6 / gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.         4WT 1   strain:AB|isolate:replicate1|ecotype:wt|age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal                 wt 1 S9 L001 R1 007 007 Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat and three repeats were performed for samll RNA sequencing.     ncRNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA HiSeq X Ten   SRP359829     wt-1_S9_L001_R1_001.fastq.gz wt-1_S9_L001_R2_001.fastq.gz fastq fastq 4820063700.0 16066879.0 wt 1 S9 L001 R1 001.fastq.gz 0:150 1:150 A:996304548;C:657334691;G:2379519106;T:786675131;N:230224 150 150     996304548 657334691 2379519106 786675131 230224 SRX14182299 SRS12005940 SRA1372890 Huazhong agricultural university|School of Life Science and Technology Huazhong agricultural university 2 0.80219 0.80319 0.60906 0.60878 0.83238 0.83303 0.52559 0.51852 150 150 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   China 2022-02-14 Multi-stage Multi-stage Gonad Reproductive System
68559 68559 SRR18028174 SRX14182298 SRS12005939 SRP359829 PRJNA807002 samll RNA seq of zebrafish gonads of wildtype and pld6 / at 22 dpf PRJNA807002 Other In this study we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 / gonad with three repetition. In pld6 / gonad small RNAs mapped to the known piRNA clusters were almost absent. Moreover piRNA clusters in pld6 / gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.         3PLD6 3   strain:AB|isolate:replicate3|ecotype:pld6 / |age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal                 pld6 3 S3 L003 R1 005 005 Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat and three repeats were performed for samll RNA sequencing.     ncRNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA HiSeq X Ten   SRP359829     pld6-3_S3_L003_R1_001.fastq.gz pld6-3_S3_L003_R2_001.fastq.gz fastq fastq 816686700.0 2722289.0 pld6 3 S3 L003 R1 001.fastq.gz 0:150 1:150 A:145681738;C:137123477;G:401610833;T:132256312;N:14340 150 150     145681738 137123477 401610833 132256312 14340 SRX14182298 SRS12005939 SRA1372890 Huazhong agricultural university|School of Life Science and Technology Huazhong agricultural university 2 0.78314 0.73942 0.07641 0.09097 0.91603 0.91545 0.6312 0.64467 150 150 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   China 2022-02-14 Multi-stage Multi-stage Gonad Reproductive System
68560 68560 SRR18028175 SRX14182297 SRS12005938 SRP359829 PRJNA807002 samll RNA seq of zebrafish gonads of wildtype and pld6 / at 22 dpf PRJNA807002 Other In this study we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 / gonad with three repetition. In pld6 / gonad small RNAs mapped to the known piRNA clusters were almost absent. Moreover piRNA clusters in pld6 / gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.         2PLD6 2   strain:AB|isolate:replicate2|ecotype:pld6 / |age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal                 pld6 2 S2 L003 R1 003 003 Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat and three repeats were performed for samll RNA sequencing.     ncRNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA HiSeq X Ten   SRP359829     pld6-2_S2_L003_R1_001.fastq.gz pld6-2_S2_L003_R2_001.fastq.gz fastq fastq 6546276900.0 21820923.0 pld6 2 S2 L003 R1 001.fastq.gz 0:150 1:150 A:1161502458;C:1095580994;G:3226725392;T:1062358099;N:109957 150 150     1161502458 1095580994 3226725392 1062358099 109957 SRX14182297 SRS12005938 SRA1372890 Huazhong agricultural university|School of Life Science and Technology Huazhong agricultural university 2 0.6471 0.593 0.07935 0.09168 0.92058 0.92005 0.53626 0.65284 150 150 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   China 2022-02-14 Multi-stage Multi-stage Gonad Reproductive System
68561 68561 SRR18028176 SRX14182296 SRS12005937 SRP359829 PRJNA807002 samll RNA seq of zebrafish gonads of wildtype and pld6 / at 22 dpf PRJNA807002 Other In this study we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 / gonad with three repetition. In pld6 / gonad small RNAs mapped to the known piRNA clusters were almost absent. Moreover piRNA clusters in pld6 / gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.         1PLD6 1   strain:AB|isolate:replicate1|ecotype:pld6 / |age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal                 pld6 1 S1 L003 R1 001 001 Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat and three repeats were performed for samll RNA sequencing.     ncRNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA HiSeq X Ten   SRP359829     pld6-1_S1_L003_R1_001.fastq.gz pld6-1_S1_L003_R2_001.fastq.gz fastq fastq 5535130200.0 18450434.0 pld6 1 S1 L003 R1 001.fastq.gz 0:150 1:150 A:1014761790;C:833992394;G:2813863824;T:872418512;N:93680 150 150     1014761790 833992394 2813863824 872418512 93680 SRX14182296 SRS12005937 SRA1372890 Huazhong agricultural university|School of Life Science and Technology Huazhong agricultural university 2 0.70358 0.73288 0.08649 0.09366 0.91066 0.90914 0.6197 0.6207 150 150 B B biological fallback assumption illumina hiseq_era unknown small_rna unknown bulk unknown unknown   China 2022-02-14 Multi-stage Multi-stage Gonad Reproductive System
74905 74905 SRR24124281 SRX19923332 SRS17275061 SRP431889 PRJNA954142 Zebrafish Gonad sequencing PRJNA954142 Other RNA sequencing of male and female gonads of zebrafish         Female Zebrafish   strain:wild type|age:90 days|sex:female|tissue:Gonad|BioSampleModel:Model organism or animal                 Femalegonad FCHGTWKCCXY L9 WHZEBjyrEAAFRABPEI 37 1 FCHGTWKCCXY L9 WHZEBjyrEAAFRABPEI 37 1 RNA was extracted from tissues of individuals using TRIzol reagent Invitrogen USA. library prep of each individual using the standard protocol provided by Illumina. 150 bp paired end Illumina reads of transcriptome were sequenced on the HiSeq2500 platform.     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP431889   loader:fastq load.py FCHGTWKCCXY_L9_WHZEBjyrEAAFRABPEI-37_1.fq FCHGTWKCCXY_L9_WHZEBjyrEAAFRABPEI-37_2.fq fastq fastq 4237141500.0 14123805.0 FCHGTWKCCXY L9 WHZEBjyrEAAFRABPEI 37 1.fq 0:150 1:150 A:1134013231;C:997301614;G:984327511;T:1121230343;N:268801 150 150     1134013231 997301614 984327511 1121230343 268801 SRX19923332 SRS17275061 SRA1618700 Madras Christian College|Zoology Madras Christian College 2 0.88523 0.88363 0.05083 0.05161 0.80381 0.80809 0.55041 0.52553 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   India 2023-04-12 Adult Adult Gonad Reproductive System
74906 74906 SRR24124282 SRX19923331 SRS17275060 SRP431889 PRJNA954142 Zebrafish Gonad sequencing PRJNA954142 Other RNA sequencing of male and female gonads of zebrafish         Male zebrafish   strain:wild type|age:90 days|sex:male|tissue:Gonad|BioSampleModel:Model organism or animal                 Malegonad FCHGTWKCCXY L9 WHZEBjyrEAAARAAPEI 27 1 FCHGTWKCCXY L9 WHZEBjyrEAAARAAPEI 27 1 RNA was extracted from tissues of individuals using TRIzol reagent Invitrogen USA. library prep of each individual using the standard protocol provided by Illumina. 150 bp paired end Illumina reads of transcriptome were sequenced on the HiSeq2500 platform.     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP431889   loader:fastq load.py FCHGTWKCCXY_L9_WHZEBjyrEAAARAAPEI-27_1.fq FCHGTWKCCXY_L9_WHZEBjyrEAAARAAPEI-27_2.fq fastq fastq 3103334700.0 10344449.0 FCHGTWKCCXY L9 WHZEBjyrEAAARAAPEI 27 1.fq 0:150 1:150 A:838963909;C:717586934;G:712046035;T:834529752;N:208070 150 150     838963909 717586934 712046035 834529752 208070 SRX19923331 SRS17275060 SRA1618700 Madras Christian College|Zoology Madras Christian College 2 0.91689 0.91731 0.06074 0.06165 0.74481 0.75032 0.53861 0.57817 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   India 2023-04-12 Adult Adult Gonad Reproductive System

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

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");;