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29 rows where experiment.library_selection = "other", technology = "unknown" and tissue_curation_coarse = "Reproductive System"

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  • Reproductive System · 29 ✖

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  • unknown · 29 ✖

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experiment.library_selection 1

  • other · 29 ✖
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
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
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

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