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368 rows where experiment.library_layout = "SINGLE", experiment.platform = "ILLUMINA" and tissue_curation_coarse = "Reproductive System"

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experiment.library_selection 10

devstage_curation >10

devstage_curation_coarse 6

experiment.library_strategy 5

technology 4

tissue_curation 2

tissue_curation_coarse 1

  • Reproductive System · 368 ✖

experiment.platform 1

  • ILLUMINA · 368 ✖

experiment.library_source 1

experiment.library_layout 1

  • SINGLE · 368 ✖
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
50 50 DRR029944 DRX026962 DRS086502 DRP004756 PRJDB3475 Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish DRP004756 Other To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.     ovulation duirng natural paring zebrafish ovary isolated from adult fish at ovulation duirng natural paring. [RNAseq] SAMD00025434   sample name:6 Ovu|strain:roy|tissue type:ovary|dev stage:adult                 Illumina HiSeq 2500 sequencing of SAMD00025434 DRX026962 6 Ovu 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004756 Illumina HiSeq 2500 sequencing of SAMD00025434       351766656.0 9771296.0 DRR029944 0:36 A:79811727;C:85391142;G:90185809;T:96371771;N:6207 36       79811727 85391142 90185809 96371771 6207 DRX026962 DRS086502 DRA003031 SHIZUOKA|Shizuoka University Shizuoka University 1 0.91956   0.01686   0.76637   0.45997   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
52 52 DRR029942 DRX026960 DRS086500 DRP004756 PRJDB3475 Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish DRP004756 Other To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.     in vivo testosterone treatment zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq replicate] SAMD00025432   sample name:4 Tes rep|strain:roy|tissue type:ovary|dev stage:adult                 Illumina HiSeq 2500 sequencing of SAMD00025432 DRX026960 4 Tes rep 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004756 Illumina HiSeq 2500 sequencing of SAMD00025432       366042528.0 10167848.0 DRR029942 0:36 A:84988522;C:88640326;G:93559022;T:98847003;N:7655 36       84988522 88640326 93559022 98847003 7655 DRX026960 DRS086500 DRA003031 SHIZUOKA|Shizuoka University Shizuoka University 1 0.91602   0.01846   0.76015   0.46475   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
53 53 DRR029941 DRX026959 DRS086499 DRP004756 PRJDB3475 Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish DRP004756 Other To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.     in vivo testosterone treatment zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq] SAMD00025431   sample name:4 Tes|strain:roy|tissue type:ovary|dev stage:adult                 Illumina HiSeq 2500 sequencing of SAMD00025431 DRX026959 4 Tes 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004756 Illumina HiSeq 2500 sequencing of SAMD00025431       1269835992.0 35273222.0 DRR029941 0:36 A:275250658;C:323605136;G:316729009;T:354204170;N:47019 36       275250658 323605136 316729009 354204170 47019 DRX026959 DRS086499 DRA003031 SHIZUOKA|Shizuoka University Shizuoka University 1 0.91467   0.02353   0.75962   0.46861   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
54 54 DRR029940 DRX026958 DRS086498 DRP004756 PRJDB3475 Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish DRP004756 Other To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.     in vivo diethylstilbestrol DES treatment zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq replicate] SAMD00025430   sample name:3 DES rep|strain:roy|tissue type:ovary|dev stage:adult                 Illumina HiSeq 2500 sequencing of SAMD00025430 DRX026958 3 DES rep 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004756 Illumina HiSeq 2500 sequencing of SAMD00025430       658651536.0 18295876.0 DRR029940                       DRX026958 DRS086498 DRA003031 SHIZUOKA|Shizuoka University Shizuoka University 1 0.89964   0.01785   0.76451   0.45872   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
55 55 DRR029939 DRX026957 DRS086497 DRP004756 PRJDB3475 Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish DRP004756 Other To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.     in vivo diethylstilbestrol DES treatment zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq] SAMD00025429   sample name:3 DES|strain:roy|tissue type:ovary|dev stage:adult                 Illumina HiSeq 2500 sequencing of SAMD00025429 DRX026957 3 DES 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004756 Illumina HiSeq 2500 sequencing of SAMD00025429       1202024016.0 33389556.0 DRR029939 0:36 A:263319430;C:305852921;G:298798093;T:334008544;N:45028 36       263319430 305852921 298798093 334008544 45028 DRX026957 DRS086497 DRA003031 SHIZUOKA|Shizuoka University Shizuoka University 1 0.90643   0.02337   0.75008   0.47587   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
56 56 DRR029938 DRX026956 DRS086496 DRP004756 PRJDB3475 Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish DRP004756 Other To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.     in vivo maturation inducing hormone DHP treatment zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq replicate] SAMD00025428   sample name:2 DHP rep|strain:roy|tissue type:ovary|dev stage:adult                 Illumina HiSeq 2500 sequencing of SAMD00025428 DRX026956 2 DHP rep 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004756 Illumina HiSeq 2500 sequencing of SAMD00025428       434243088.0 12062308.0 DRR029938 0:36 A:99859342;C:105890785;G:110526688;T:117957580;N:8693 36       99859342 105890785 110526688 117957580 8693 DRX026956 DRS086496 DRA003031 SHIZUOKA|Shizuoka University Shizuoka University 1 0.91529   0.02061   0.7595   0.45809   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
57 57 DRR029937 DRX026955 DRS086495 DRP004756 PRJDB3475 Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish DRP004756 Other To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.     in vivo maturation inducing hormone DHP treatment zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq] SAMD00025427   sample name:2 DHP|strain:roy|tissue type:ovary|dev stage:adult                 Illumina HiSeq 2500 sequencing of SAMD00025427 DRX026955 2 DHP 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004756 Illumina HiSeq 2500 sequencing of SAMD00025427       1463868972.0 40663027.0 DRR029937 0:36 A:316060780;C:369221844;G:372845502;T:405685804;N:55042 36       316060780 369221844 372845502 405685804 55042 DRX026955 DRS086495 DRA003031 SHIZUOKA|Shizuoka University Shizuoka University 1 0.91556   0.01967   0.76621   0.46541   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
58 58 DRR029936 DRX026954 DRS086494 DRP004756 PRJDB3475 Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish DRP004756 Other To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.     in vivo ethanol treatment zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq replicate] SAMD00025426   sample name:1 EtOH rep|strain:roy|tissue type:ovary|dev stage:adult                 Illumina HiSeq 2500 sequencing of SAMD00025426 DRX026954 1 EtOH rep 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004756 Illumina HiSeq 2500 sequencing of SAMD00025426       438020208.0 12167228.0 DRR029936 0:36 A:101672612;C:105602774;G:110120652;T:120615069;N:9101 36       101672612 105602774 110120652 120615069 9101 DRX026954 DRS086494 DRA003031 SHIZUOKA|Shizuoka University Shizuoka University 1 0.90777   0.01929   0.7652   0.45988   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
59 59 DRR029935 DRX026953 DRS086493 DRP004756 PRJDB3475 Identification of ovulation inducing genes selected by the method for in vivo induction of oocyte maturation and ovulation in zebrafish DRP004756 Other To identify ovulation inducing genes RNAseq analysis was carried out using samples prepared by in vivo assay system in zebrafish.     in vivo ethanol treatment zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq] SAMD00025425   sample name:1 EtOH|strain:roy|tissue type:ovary|dev stage:adult                 Illumina HiSeq 2500 sequencing of SAMD00025425 DRX026953 1 EtOH 1 1   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004756 Illumina HiSeq 2500 sequencing of SAMD00025425       1365603372.0 37933427.0 DRR029935 0:36 A:299786286;C:345487829;G:342408447;T:377870789;N:50021 36       299786286 345487829 342408447 377870789 50021 DRX026953 DRS086493 DRA003031 SHIZUOKA|Shizuoka University Shizuoka University 1 0.91103   0.02142   0.75402   0.46574   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
174 174 DRR084198 DRX078029 DRS086523 DRP004758 PRJDB5490 Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish DRP004758 Other Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.     in vivo testosterone treatment zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq replicate2] SAMD00073605   sample name:TES1 4th|replicate:biological replicate 2                 Illumina HiSeq 2500 sequencing of SAMD00073605 DRX078029 zebrafish ovary isolated from adult fish in vivo testosterone treatment. [RNAseq replicate2] 1 Agilent SureSelect Strand Specific RNA Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004758 Illumina HiSeq 2500 sequencing of SAMD00073605       1382763132.0 38410087.0 DRR084198 0:36 A:314367195;C:333340483;G:353519828;T:378654329;N:2881297 36       314367195 333340483 353519828 378654329 2881297 DRX078029 DRS086523 DRA005484 SHIZUOKA|Shizuoka University Shizuoka University 1 0.90366   0.02033   0.77104   0.46543   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
176 176 DRR084196 DRX078027 DRS086521 DRP004758 PRJDB5490 Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish DRP004758 Other Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.     in vivo ethanol treatment zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq replicate2] SAMD00073603   sample name:Et 4th|replicate:biological replicate 2                 Illumina HiSeq 2500 sequencing of SAMD00073603 DRX078027 zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq replicate2] 1 Agilent SureSelect Strand Specific RNA Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004758 Illumina HiSeq 2500 sequencing of SAMD00073603       1456791660.0 40466435.0 DRR084196 0:36 A:336533534;C:355126203;G:368021063;T:394179246;N:2931614 36       336533534 355126203 368021063 394179246 2931614 DRX078027 DRS086521 DRA005484 SHIZUOKA|Shizuoka University Shizuoka University 1 0.89408   0.02082   0.77027   0.45866   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
177 177 DRR084195 DRX078026 DRS086520 DRP004758 PRJDB5490 Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish DRP004758 Other Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.     natural paring late sample zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq replicate2] SAMD00073602   sample name:O 4th|replicate:biological replicate 2                 Illumina HiSeq 2500 sequencing of SAMD00073602 DRX078026 zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq replicate2] 1 Agilent SureSelect Strand Specific RNA Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004758 Illumina HiSeq 2500 sequencing of SAMD00073602       1627945092.0 45220697.0 DRR084195 0:36 A:381205209;C:392853175;G:410714269;T:439790560;N:3381879 36       381205209 392853175 410714269 439790560 3381879 DRX078026 DRS086520 DRA005484 SHIZUOKA|Shizuoka University Shizuoka University 1 0.89419   0.02159   0.76848   0.46407   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
178 178 DRR084194 DRX078025 DRS086519 DRP004758 PRJDB5490 Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish DRP004758 Other Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.     in vivo maturation inducing hormone DHP treatment zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq replicate2] SAMD00073601   sample name:DHP 4th|replicate:biological replicate 2                 Illumina HiSeq 2500 sequencing of SAMD00073601 DRX078025 zebrafish ovary isolated from adult fish in vivo maturation inducing hormone DHP treatment. [RNAseq replicate2] 1 Agilent SureSelect Strand Specific RNA Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004758 Illumina HiSeq 2500 sequencing of SAMD00073601       969680196.0 26935561.0 DRR084194 0:36 A:223558856;C:233793515;G:244712298;T:265549055;N:2066472 36       223558856 233793515 244712298 265549055 2066472 DRX078025 DRS086519 DRA005484 SHIZUOKA|Shizuoka University Shizuoka University 1 0.90178   0.02203   0.76579   0.46491   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
179 179 DRR084193 DRX078024 DRS086518 DRP004758 PRJDB5490 Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish DRP004758 Other Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.     in vivo diethylstilbestrol DES treatment zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq replicate2] SAMD00073600   sample name:DES 4th|replicate:biological replicate 2                 Illumina HiSeq 2500 sequencing of SAMD00073600 DRX078024 zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq replicate2] 1 Agilent SureSelect Strand Specific RNA Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004758 Illumina HiSeq 2500 sequencing of SAMD00073600       825301296.0 22925036.0 DRR084193 0:36 A:189771874;C:198593952;G:209666041;T:225480165;N:1789264 36       189771874 198593952 209666041 225480165 1789264 DRX078024 DRS086518 DRA005484 SHIZUOKA|Shizuoka University Shizuoka University 1 0.90036   0.0197   0.7721   0.45773   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
180 180 DRR084192 DRX078023 DRS086517 DRP004758 PRJDB5490 Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish DRP004758 Other Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.     natural paring late sample zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq replicate1] SAMD00073599   sample name:O|replicate:biological replicate 1                 Illumina HiSeq 2500 sequencing of SAMD00073599 DRX078023 zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq replicate1] 1 Agilent SureSelect Strand Specific RNA Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004758 Illumina HiSeq 2500 sequencing of SAMD00073599       1474870356.0 40968621.0 DRR084192 0:36 A:334130826;C:361572335;G:369758908;T:409173431;N:234856 36       334130826 361572335 369758908 409173431 234856 DRX078023 DRS086517 DRA005484 SHIZUOKA|Shizuoka University Shizuoka University 1 0.91516   0.02086   0.76792   0.47914   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
182 182 DRR084190 DRX078021 DRS086515 DRP004758 PRJDB5490 Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish DRP004758 Other Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.     in vivo maturation inducing hormone DHP treatment zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq replicate1] SAMD00073597   sample name:DHP|replicate:biological replicate 1                 Illumina HiSeq 2500 sequencing of SAMD00073597 DRX078021 zebrafish ovary isolated from adult fish in vivo maturation inducing hormone DHP treatment. [RNAseq replicate1] 1 Agilent SureSelect Strand Specific RNA Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004758 Illumina HiSeq 2500 sequencing of SAMD00073597       1527194556.0 42422071.0 DRR084190 0:36 A:352068936;C:371030475;G:383086948;T:420761508;N:246689 36       352068936 371030475 383086948 420761508 246689 DRX078021 DRS086515 DRA005484 SHIZUOKA|Shizuoka University Shizuoka University 1 0.91815   0.02248   0.76209   0.46867   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
183 183 DRR084189 DRX078020 DRS086514 DRP004758 PRJDB5490 Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish DRP004758 Other Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.     in vivo testosterone treatment zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq replicate1] SAMD00073596   sample name:TES|replicate:biological replicate 1                 Illumina HiSeq 2500 sequencing of SAMD00073596 DRX078020 zebrafish ovary isolated from adult fish in vivo testosterone treatment. [RNAseq replicate1] 1 Agilent SureSelect Strand Specific RNA Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004758 Illumina HiSeq 2500 sequencing of SAMD00073596       1403618796.0 38989411.0 DRR084189 0:36 A:321063874;C:342718133;G:352434647;T:387171455;N:230687 36       321063874 342718133 352434647 387171455 230687 DRX078020 DRS086514 DRA005484 SHIZUOKA|Shizuoka University Shizuoka University 1 0.91583   0.02212   0.76073   0.47596   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
184 184 DRR084188 DRX078019 DRS086513 DRP004758 PRJDB5490 Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish DRP004758 Other Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.     in vivo diethylstilbestrol DES treatment zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq replicate1] SAMD00073595   sample name:DES|replicate:biological replicate 1                 Illumina HiSeq 2500 sequencing of SAMD00073595 DRX078019 zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq replicate1] 1 Agilent SureSelect Strand Specific RNA Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004758 Illumina HiSeq 2500 sequencing of SAMD00073595       1532053512.0 42557042.0 DRR084188 0:36 A:342701220;C:372650449;G:392432461;T:424025702;N:243680 36       342701220 372650449 392432461 424025702 243680 DRX078019 DRS086513 DRA005484 SHIZUOKA|Shizuoka University Shizuoka University 1 0.91276   0.01965   0.77358   0.46461   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
185 185 DRR084187 DRX078018 DRS086512 DRP004758 PRJDB5490 Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish DRP004758 Other Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.     in vivo ethanol treatment zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq replicate1] SAMD00073594   sample name:EtOH|replicate:biological replicate 1                 Illumina HiSeq 2500 sequencing of SAMD00073594 DRX078018 zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq replicate1] 1 Agilent SureSelect Strand Specific RNA Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004758 Illumina HiSeq 2500 sequencing of SAMD00073594       1152032724.0 32000909.0 DRR084187 0:36 A:265166034;C:279617628;G:285136940;T:321928656;N:183466 36       265166034 279617628 285136940 321928656 183466 DRX078018 DRS086512 DRA005484 SHIZUOKA|Shizuoka University Shizuoka University 1 0.90791   0.02405   0.75972   0.48931   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2019-01-23 Adult Adult Gonad Reproductive System
25293 25293 SRR25764131 SRX21486791 SRS18719090 SRP457111 PRJNA1009808 Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq] GSE241754 Transcriptome Analysis Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. parent bioproject:PRJNA1009800 pubmed:39402326   WT egg 0 hpf tRNA seq rep2 GSM7734772   source name:Unfertilized egg|strain:TLAB strain|tissue:Unfertilized egg|developmental stage:unfertilized egg 0 hpf|genotype:WT|geo loc name:missing|collection date:missing WT egg 0 hpf tRNA seq rep2 Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters species Drer cluster id 0.93 min cov 0.001 max mismatches 0.075 control condition Egg deconv cov ratio 0.4 remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts Unfertilized egg unperturbed growth conditions in E3 medium for zebrafish embryos. 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle. strain:TLAB strain|tissue:Unfertilized egg|developmental stage:unfertilized egg 0 hpf|genotype:WT GSM7734772 GSM7734772: WT egg 0 hpf tRNA seq rep2; Danio rerio; ncRNA Seq GSM7734772 r1 GSM7734772 1 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP457111     WT_tRNA_egg_2.fastq.gz fastq 206374994.0 3181706.0 GSM7734772 r1 0:64.86 A:41195250;C:56578032;G:56479855;T:52121365;N:492 64       41195250 56578032 56479855 52121365 492 SRX21486791 SRS18719090 SRA1700461 Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry Max Planck Institute of Biochemistry 1 0.28659   0.02017   0.9207   0.48536   78   B   usable mapping rate illumina nextseq 5prime size_fractionation unknown bulk unknown unknown   Germany 2023-08-28 Zygote Embryo Oocyte Reproductive System
25294 25294 SRR25764132 SRX21486790 SRS18719089 SRP457111 PRJNA1009808 Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq] GSE241754 Transcriptome Analysis Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. parent bioproject:PRJNA1009800 pubmed:39402326   WT egg 0 hpf tRNA seq rep1 GSM7734771   source name:Unfertilized egg|strain:TLAB strain|tissue:Unfertilized egg|developmental stage:unfertilized egg 0 hpf|genotype:WT|geo loc name:missing|collection date:missing WT egg 0 hpf tRNA seq rep1 Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.2 using the parameters species Drer cluster id 0.93 min cov 0.001 max mismatches 0.075 control condition Egg deconv cov ratio 0.4 remap mismatches 0.075. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters and on read counts summed by isotype. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated tRNA transcript resad counts Unfertilized egg unperturbed growth conditions in E3 medium for zebrafish embryos. 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq Embryos were grown in standard housing conditions namely28°C at a 14/10 hour light/dark cycle. strain:TLAB strain|tissue:Unfertilized egg|developmental stage:unfertilized egg 0 hpf|genotype:WT GSM7734771 GSM7734771: WT egg 0 hpf tRNA seq rep1; Danio rerio; ncRNA Seq GSM7734771 r1 GSM7734771 1 50 whole embryos were collected per sample and immediately lysed in 800uL LiDS/LET buffer5% Lithium dodecyl sulfate in 20 mM Tris HCl pH=7.4 100 mM LiCl 2 mM EDTA 5 mM DTT pH 7.4. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens 2021 2022 and sequenced on an Illumina NextSeq 500 platform. mim tRNAseq   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP457111     WT_tRNA_egg_1.fastq.gz fastq 86021968.0 1304769.0 GSM7734771 r1 0:65.93 A:17511521;C:23474625;G:23300759;T:21734864;N:199 65       17511521 23474625 23300759 21734864 199 SRX21486790 SRS18719089 SRA1700461 Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry Max Planck Institute of Biochemistry 1 0.29829   0.02027   0.92245   0.48877   74   B   usable mapping rate illumina nextseq 5prime size_fractionation unknown bulk unknown unknown   Germany 2023-08-28 Zygote Embryo Oocyte Reproductive System
29259 29259 SRR27336917 SRX23013778 SRS19977075 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 PaternalKO gonads 31dpf rep2 miR214 PaternalKO gonads 31dpf rep2   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalKO|biological replicate:rep2|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A11 miR214 PaternalKO gonads 31dpf rep2 miR214 PaternalKO gonads 31dpf rep2 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_PaternalKO_gonads_31dpf_rep2.fastq.gz fastq 2327996832.0 27714248.0 miR214 PaternalKO gonads 31dpf rep2.fastq.gz 0:84 A:602135965;C:552786494;G:537368428;T:635697339;N:8606 84       602135965 552786494 537368428 635697339 8606 SRX23013778 SRS19977075 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95369   0.06146   0.69203   0.47259   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29260 29260 SRR27336918 SRX23013777 SRS19977074 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 PaternalKO gonads 31dpf rep1 miR214 PaternalKO gonads 31dpf rep1   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalKO|biological replicate:rep1|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A10 miR214 PaternalKO gonads 31dpf rep1 miR214 PaternalKO gonads 31dpf rep1 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_PaternalKO_gonads_31dpf_rep1.fastq.gz fastq 2500978452.0 29773553.0 miR214 PaternalKO gonads 31dpf rep1.fastq.gz 0:84 A:646162933;C:593855971;G:578265372;T:682684551;N:9625 84       646162933 593855971 578265372 682684551 9625 SRX23013777 SRS19977074 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95147   0.05972   0.69071   0.47043   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29261 29261 SRR27336919 SRX23013776 SRS19977073 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 maternalHET gonads 31dpf rep4 miR214 maternalHET gonads 31dpf rep4   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalHET|biological replicate:rep4|number of gonads:7 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A9 miR214 maternalHET gonads 31dpf rep4 miR214 maternalHET gonads 31dpf rep4 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_maternalHET_gonads_31dpf_rep4.fastq.gz fastq 2365480908.0 28160487.0 miR214 maternalHET gonads 31dpf rep4.fastq.gz 0:84 A:613121312;C:560582165;G:549338096;T:642429834;N:9501 84       613121312 560582165 549338096 642429834 9501 SRX23013776 SRS19977073 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95304   0.05342   0.7108   0.46822   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29262 29262 SRR27336920 SRX23013775 SRS19977072 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 maternalHET gonads 31dpf rep3 miR214 maternalHET gonads 31dpf rep3   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalHET|biological replicate:rep3|number of gonads:7 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A8 miR214 maternalHET gonads 31dpf rep3 miR214 maternalHET gonads 31dpf rep3 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_maternalHET_gonads_31dpf_rep3.fastq.gz fastq 2537794644.0 30211841.0 miR214 maternalHET gonads 31dpf rep3.fastq.gz 0:84 A:658687178;C:600742464;G:585643169;T:692712057;N:9776 84       658687178 600742464 585643169 692712057 9776 SRX23013775 SRS19977072 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95177   0.06701   0.68195   0.47393   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29263 29263 SRR27336921 SRX23013774 SRS19977071 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 maternalHET gonads 31dpf rep2 miR214 maternalHET gonads 31dpf rep2   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalHET|biological replicate:rep2|number of gonads:7 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A7 miR214 maternalHET gonads 31dpf rep2 miR214 maternalHET gonads 31dpf rep2 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_maternalHET_gonads_31dpf_rep2.fastq.gz fastq 2417384424.0 28778386.0 miR214 maternalHET gonads 31dpf rep2.fastq.gz 0:84 A:625935186;C:574179061;G:560498085;T:656762980;N:9112 84       625935186 574179061 560498085 656762980 9112 SRX23013774 SRS19977071 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95259   0.05852   0.6981   0.47435   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29264 29264 SRR27336922 SRX23013773 SRS19977070 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 maternalHET gonads 31dpf rep1 miR214 maternalHET gonads 31dpf rep1   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalHET|biological replicate:rep1|number of gonads:7 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A6 miR214 maternalHET gonads 31dpf rep1 miR214 maternalHET gonads 31dpf rep1 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_maternalHET_gonads_31dpf_rep1.fastq.gz fastq 2330886180.0 27748645.0 miR214 maternalHET gonads 31dpf rep1.fastq.gz 0:84 A:601589571;C:554105326;G:542789267;T:632393158;N:8858 84       601589571 554105326 542789267 632393158 8858 SRX23013773 SRS19977070 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95338   0.05239   0.71366   0.47291   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29265 29265 SRR27336923 SRX23013772 SRS19977069 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 maternalKO gonads 31dpf rep4 miR214 maternalKO gonads 31dpf rep4   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalKO|biological replicate:rep4|number of gonads:8 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A5 miR214 maternalKO gonads 31dpf rep4 miR214 maternalKO gonads 31dpf rep4 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_maternalKO_gonads_31dpf_rep4.fastq.gz fastq 2340233784.0 27859926.0 miR214 maternalKO gonads 31dpf rep4.fastq.gz 0:84 A:606735187;C:553647808;G:539865459;T:639976430;N:8900 84       606735187 553647808 539865459 639976430 8900 SRX23013772 SRS19977069 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95406   0.06415   0.68225   0.47695   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29266 29266 SRR27336924 SRX23013771 SRS19977068 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 maternalKO gonads 31dpf rep3 miR214 maternalKO gonads 31dpf rep3   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalKO|biological replicate:rep3|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A4 miR214 maternalKO gonads 31dpf rep3 miR214 maternalKO gonads 31dpf rep3 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_maternalKO_gonads_31dpf_rep3.fastq.gz fastq 2058505512.0 24506018.0 miR214 maternalKO gonads 31dpf rep3.fastq.gz 0:84 A:537425814;C:485664494;G:471526682;T:563881213;N:7309 84       537425814 485664494 471526682 563881213 7309 SRX23013771 SRS19977068 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95296   0.06728   0.69266   0.47627   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29267 29267 SRR27336925 SRX23013770 SRS19977067 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 PaternalHET gonads 31dpf rep4 miR214 PaternalHET gonads 31dpf rep4   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalHET|biological replicate:rep4|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A17 miR214 PaternalHET gonads 31dpf rep4 miR214 PaternalHET gonads 31dpf rep4 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_PaternalHET_gonads_31dpf_rep4.fastq.gz fastq 3001613328.0 35733492.0 miR214 PaternalHET gonads 31dpf rep4.fastq.gz 0:84 A:778860501;C:711155422;G:688784969;T:822801157;N:11279 84       778860501 711155422 688784969 822801157 11279 SRX23013770 SRS19977067 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95361   0.05653   0.7051   0.48382   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29268 29268 SRR27336926 SRX23013769 SRS19977066 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 PaternalHET gonads 31dpf rep3 miR214 PaternalHET gonads 31dpf rep3   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalHET|biological replicate:rep3|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A16 miR214 PaternalHET gonads 31dpf rep3 miR214 PaternalHET gonads 31dpf rep3 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_PaternalHET_gonads_31dpf_rep3.fastq.gz fastq 3053630664.0 36352746.0 miR214 PaternalHET gonads 31dpf rep3.fastq.gz 0:84 A:785219727;C:726431662;G:713454025;T:828513556;N:11694 84       785219727 726431662 713454025 828513556 11694 SRX23013769 SRS19977066 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95309   0.04588   0.71997   0.46447   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29269 29269 SRR27336927 SRX23013768 SRS19977065 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 PaternalHET gonads 31dpf rep2 miR214 PaternalHET gonads 31dpf rep2   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalHET|biological replicate:rep2|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A15 miR214 PaternalHET gonads 31dpf rep2 miR214 PaternalHET gonads 31dpf rep2 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_PaternalHET_gonads_31dpf_rep2.fastq.gz fastq 3063695208.0 36472562.0 miR214 PaternalHET gonads 31dpf rep2.fastq.gz 0:84 A:784924646;C:728941687;G:720847462;T:828969510;N:11903 84       784924646 728941687 720847462 828969510 11903 SRX23013768 SRS19977065 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95413   0.04739   0.71936   0.4704   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29270 29270 SRR27336928 SRX23013767 SRS19977064 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 PaternalHET gonads 31dpf rep1 miR214 PaternalHET gonads 31dpf rep1   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalHET|biological replicate:rep1|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:heterozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A14 miR214 PaternalHET gonads 31dpf rep1 miR214 PaternalHET gonads 31dpf rep1 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_PaternalHET_gonads_31dpf_rep1.fastq.gz fastq 2699154024.0 32132786.0 miR214 PaternalHET gonads 31dpf rep1.fastq.gz 0:84 A:694174797;C:642049572;G:627991562;T:734927762;N:10331 84       694174797 642049572 627991562 734927762 10331 SRX23013767 SRS19977064 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95518   0.05525   0.70285   0.47695   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29271 29271 SRR27336929 SRX23013766 SRS19977063 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 PaternalKO gonads 31dpf rep4 miR214 PaternalKO gonads 31dpf rep4   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalKO|biological replicate:rep4|number of gonads:8 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A13 miR214 PaternalKO gonads 31dpf rep4 miR214 PaternalKO gonads 31dpf rep4 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_PaternalKO_gonads_31dpf_rep4.fastq.gz fastq 2514248016.0 29931524.0 miR214 PaternalKO gonads 31dpf rep4.fastq.gz 0:84 A:648908956;C:598837726;G:580002743;T:686488678;N:9913 84       648908956 598837726 580002743 686488678 9913 SRX23013766 SRS19977063 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.94978   0.06951   0.67896   0.47686   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29272 29272 SRR27336930 SRX23013765 SRS19977062 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 PaternalKO gonads 31dpf rep3 miR214 PaternalKO gonads 31dpf rep3   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:PaternalKO|biological replicate:rep3|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a heterozygous female crossed to a homozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A12 miR214 PaternalKO gonads 31dpf rep3 miR214 PaternalKO gonads 31dpf rep3 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_PaternalKO_gonads_31dpf_rep3.fastq.gz fastq 2499529200.0 29756300.0 miR214 PaternalKO gonads 31dpf rep3.fastq.gz 0:84 A:642490769;C:597403823;G:580565141;T:679060154;N:9313 84       642490769 597403823 580565141 679060154 9313 SRX23013765 SRS19977062 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95284   0.05602   0.70289   0.47154   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29273 29273 SRR27336931 SRX23013764 SRS19977061 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 maternalKO gonads 31dpf rep2 miR214 maternalKO gonads 31dpf rep2   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalKO|biological replicate:rep2|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A3 miR214 maternalKO gonads 31dpf rep2 miR214 maternalKO gonads 31dpf rep2 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_maternalKO_gonads_31dpf_rep2.fastq.gz fastq 2529742404.0 30115981.0 miR214 maternalKO gonads 31dpf rep2.fastq.gz 0:84 A:652091166;C:600932059;G:589100617;T:687608862;N:9700 84       652091166 600932059 589100617 687608862 9700 SRX23013764 SRS19977061 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95498   0.05524   0.70366   0.47319   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29274 29274 SRR27336932 SRX23013763 SRS19977060 SRP479907 PRJNA1056454 miR214 regulates sex determination through gsdf in zebrafish PRJNA1056454 Other Sex determination is a variable and complex mechanism yet it can be found all over the plant and animal kingdoms. It creates two morphological different outcomes from one and the same species. Our work demonstrates the involvement of a non coding RNA in this process for the teleost Danio rerio. Although we were not able to understand the full mechanism behind it we can provide a piece of the puzzle which once again highlights the complexity and flexibility of sex determination.     CrisprCas9 generated using 2 sgRNAs >F3 crossed toTgvasa:eGFP miR214 maternalKO gonads 31dpf rep1 miR214 maternalKO gonads 31dpf rep1   strain:mz 06de tgvasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:27 dpf|dev stage:27 dpf|sex:not applicable|tissue:gonads|parental ko:maternalKO|biological replicate:rep1|number of gonads:9 gonads|birth date:21.09.2018|collection date:not applicable|genotype:homozygous mutation for miR 214 from a homozygous female crossed to a heterozygous male|geo loc name:not applicable|growth protocol:standard|phenotype:n1|sample type:tissue|BioSampleModel:Model organism or animal                 = xlfn.CONCAT"mrna sequencing of zebrafish: " A2 miR214 maternalKO gonads 31dpf rep1 miR214 maternalKO gonads 31dpf rep1 NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following Illuminas standard protocol Part # 15031047 Rev E. Libraries were prepared with a starting amount of 193 ng and amplified in 13 PCR cycles Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2 0 Fluorometer Life technologies. All 16 samples were pooled in equimolar ratio and sequenced on 1 NextSeq 500 Highoutput FC SR for 1 x 84 cycles plus 7 cycles for the index read.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP479907     miR214_maternalKO_gonads_31dpf_rep1.fastq.gz fastq 2310878136.0 27510454.0 miR214 maternalKO gonads 31dpf rep1.fastq.gz 0:84 A:598541924;C:547875391;G:533137786;T:631314274;N:8761 84       598541924 547875391 533137786 631314274 8761 SRX23013763 SRS19977060 SRA1775014 Rene Ketting group|Ketting Lab Rene Ketting group 1 0.95279   0.06446   0.68757   0.4758   84   B   usable mapping rate illumina nextseq unknown poly_a trueseq bulk unknown unknown   Germany 2023-12-24 Larval Larval Gonad Reproductive System
29720 29720 SRR27485665 SRX23156884 SRS20107305 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           ovary R3   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|replicate:3|BioSampleModel:Model organism or animal                 mRNA seq of zebrafish: ovary rep4 EV06008 EV06008 RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP482074     EV06008.R1.fastq.gz fastq 585955025.0 7769646.0 EV06008.R1.fastq.gz 0:75.42 A:167210227;C:106735220;G:128095616;T:183896888;N:17074 75       167210227 106735220 128095616 183896888 17074 SRX23156884 SRS20107305 SRA1783314 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.85544   0.05096   0.78441   0.53007   76   B   usable mapping rate illumina nextseq 3prime poly_a lexogen bulk unknown unknown   Austria 2024-01-11 Adult Adult Gonad Reproductive System
29731 29731 SRR27485676 SRX23156873 SRS20107294 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           ovary R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|replicate:2|BioSampleModel:Model organism or animal                 mRNA seq of zebrafish: ovary rep4 EV06001 EV06001 RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP482074     EV06001.R1.fastq.gz fastq 685280356.0 9098789.0 EV06001.R1.fastq.gz 0:75.32 A:194596366;C:122550539;G:153504013;T:214558450;N:70988 75       194596366 122550539 153504013 214558450 70988 SRX23156873 SRS20107294 SRA1783314 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.8304   0.04498   0.80166   0.5028   74   B   usable mapping rate illumina nextseq 3prime poly_a lexogen bulk unknown unknown   Austria 2024-01-11 Adult Adult Gonad Reproductive System
29738 29738 SRR27477298 SRX23148649 SRS20099367 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           ovary R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|replicate:4|BioSampleModel:Model organism or animal                 mRNA seq of zebrafish: ovary rep4 EV09001 EV09001 RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP482074     EV09001.R1.fastq.gz fastq 456295310.0 6058854.0 EV09001.R1.fastq.gz 0:75.31 A:135579999;C:83364677;G:101608151;T:135700843;N:41640 75       135579999 83364677 101608151 135700843 41640 SRX23148649 SRS20099367 SRA1782413 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.85088   0.05876   0.7791   0.50948   75   B   usable mapping rate illumina nextseq 3prime poly_a lexogen bulk unknown unknown   Austria 2024-01-10 Adult Adult Gonad Reproductive System
29765 29765 SRR27437485 SRX23109812 SRS20064566 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           ovary BS R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: ovary BS rep3 EV04017 EV04017 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04017.R1.fastq.gz fastq 576584540.0 4118461.0 EV04017.R1.fastq.gz 0:140 A:149516980;C:91163801;G:169046762;T:166831111;N:25886 140       149516980 91163801 169046762 166831111 25886 SRX23109812 SRS20064566 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.0   0.0   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Adult Adult Gonad Reproductive System
29776 29776 SRR27437496 SRX23109801 SRS20064555 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           ovary DM R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: ovary DM rep3 EV04016 EV04016 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04016.R1.fastq.gz fastq 635752880.0 4541092.0 EV04016.R1.fastq.gz 0:140 A:160072248;C:143996869;G:189137330;T:142516059;N:30374 140       160072248 143996869 189137330 142516059 30374 SRX23109801 SRS20064555 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 1e-05   0.0   0.99997   1.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Adult Adult Gonad Reproductive System
29777 29777 SRR27437497 SRX23109800 SRS20064554 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           ovary mock R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: ovary mock rep3 EV04015 EV04015 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04015.R1.fastq.gz fastq 489700680.0 3497862.0 EV04015.R1.fastq.gz 0:140 A:126641754;C:126582886;G:130564204;T:105889815;N:22021 140       126641754 126582886 130564204 105889815 22021 SRX23109800 SRS20064554 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 6e-05   0.0   0.99983   0.55555   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Adult Adult Gonad Reproductive System
29786 29786 SRR27435871 SRX23108225 SRS20063062 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           ovary BS R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: ovary BS rep4 EV08003 EV08003 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV08003.R1.fastq.gz fastq 571689580.0 4083497.0 EV08003.R1.fastq.gz 0:140 A:141414131;C:88722455;G:138790445;T:202723075;N:39474 140       141414131 88722455 138790445 202723075 39474 SRX23108225 SRS20063062 SRA1780265 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 3e-05   0.0   0.99991   0.75   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-05 Adult Adult Gonad Reproductive System
29797 29797 SRR27435882 SRX23108214 SRS20063050 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           ovary DM R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: ovary DM rep4 EV08002 EV08002 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV08002.R1.fastq.gz fastq 668593800.0 4775670.0 EV08002.R1.fastq.gz 0:140 A:164584224;C:175789134;G:175538168;T:152637106;N:45168 140       164584224 175789134 175538168 152637106 45168 SRX23108214 SRS20063050 SRA1780265 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.00525   2e-05   0.99192   0.63501   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-05 Adult Adult Gonad Reproductive System
29798 29798 SRR27435883 SRX23108213 SRS20063051 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           ovary mock R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: ovary mock rep4 EV08001 EV08001 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV08001.R1.fastq.gz fastq 753247460.0 5380339.0 EV08001.R1.fastq.gz 0:140 A:183862675;C:196453674;G:197604061;T:175275086;N:51964 140       183862675 196453674 197604061 175275086 51964 SRX23108213 SRS20063051 SRA1780265 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.00754   4e-05   0.98957   0.51048   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-05 Adult Adult Gonad Reproductive System
30755 30755 SRR28348921 SRX23954975 SRS20755396 SRP495323 PRJNA1088158 Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis. GSE261646 Transcriptome Analysis The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…   pubmed:39302832   Zebrafish Oocyte Stage IV rep2 GSM8147872   source name:Oocyte|tissue:Oocyte|developmental stage:Stage IV|genotype:AB TF and TLF|geo loc name:missing|collection date:missing Zebrafish Oocyte Stage IV rep2 Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates Oocyte   Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.   tissue:Oocyte|developmental stage:Stage IV|genotype:AB TF and TLF GSM8147872 GSM8147872: Zebrafish Oocyte Stage IV rep2; Danio rerio; RNA Seq GSM8147872 r1 GSM8147872 1 Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP495323     Z_oocyte_stage_4_2_Pa.fastq fastq 2456514332.0 32322557.0 GSM8147872 r1 0:76 A:588246161;C:609187233;G:593122683;T:665837765;N:120490 76       588246161 609187233 593122683 665837765 120490 SRX23954975 SRS20755396 SRA1824599 Computational Biology, Stowers Institute for Medical Research Computational Biology, Stowers Institute for Medical Research                       B   usable mapping rate illumina nextseq unknown cdna_unspecified trueseq bulk bulk bulk   United States 2024-03-14 Multi-stage Embryo Oocyte Reproductive System
30756 30756 SRR28348922 SRX23954974 SRS20755395 SRP495323 PRJNA1088158 Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis. GSE261646 Transcriptome Analysis The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…   pubmed:39302832   Zebrafish Oocyte Stage IV rep1 GSM8147871   source name:Oocyte|tissue:Oocyte|developmental stage:Stage IV|genotype:AB TF and TLF|geo loc name:missing|collection date:missing Zebrafish Oocyte Stage IV rep1 Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates Oocyte   Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.   tissue:Oocyte|developmental stage:Stage IV|genotype:AB TF and TLF GSM8147871 GSM8147871: Zebrafish Oocyte Stage IV rep1; Danio rerio; RNA Seq GSM8147871 r1 GSM8147871 1 Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP495323     Z_oocyte_stage_4_1_Pa.fastq fastq 2650784696.0 34878746.0 GSM8147871 r1 0:76 A:649971632;C:640667370;G:632570967;T:727447552;N:127175 76       649971632 640667370 632570967 727447552 127175 SRX23954974 SRS20755395 SRA1824599 Computational Biology, Stowers Institute for Medical Research Computational Biology, Stowers Institute for Medical Research                       B   usable mapping rate illumina nextseq unknown cdna_unspecified trueseq bulk bulk bulk   United States 2024-03-14 Multi-stage Embryo Oocyte Reproductive System
30757 30757 SRR28348923 SRX23954973 SRS20755394 SRP495323 PRJNA1088158 Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis. GSE261646 Transcriptome Analysis The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…   pubmed:39302832   Zebrafish Oocyte Stage III rep2 GSM8147870   source name:Oocyte|tissue:Oocyte|developmental stage:Stage III|genotype:AB TF and TLF|geo loc name:missing|collection date:missing Zebrafish Oocyte Stage III rep2 Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates Oocyte   Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.   tissue:Oocyte|developmental stage:Stage III|genotype:AB TF and TLF GSM8147870 GSM8147870: Zebrafish Oocyte Stage III rep2; Danio rerio; RNA Seq GSM8147870 r1 GSM8147870 1 Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP495323     Z_oocyte_stage_3_2_Pa.fastq fastq 2809957956.0 36973131.0 GSM8147870 r1 0:76 A:679041537;C:690924547;G:702857353;T:736996218;N:138301 76       679041537 690924547 702857353 736996218 138301 SRX23954973 SRS20755394 SRA1824599 Computational Biology, Stowers Institute for Medical Research Computational Biology, Stowers Institute for Medical Research                       B   usable mapping rate illumina nextseq unknown cdna_unspecified trueseq bulk bulk bulk   United States 2024-03-14 Multi-stage Embryo Oocyte Reproductive System
30758 30758 SRR28348924 SRX23954972 SRS20755393 SRP495323 PRJNA1088158 Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis. GSE261646 Transcriptome Analysis The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…   pubmed:39302832   Zebrafish Oocyte Stage III rep1 GSM8147869   source name:Oocyte|tissue:Oocyte|developmental stage:Stage III|genotype:AB TF and TLF|geo loc name:missing|collection date:missing Zebrafish Oocyte Stage III rep1 Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates Oocyte   Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.   tissue:Oocyte|developmental stage:Stage III|genotype:AB TF and TLF GSM8147869 GSM8147869: Zebrafish Oocyte Stage III rep1; Danio rerio; RNA Seq GSM8147869 r1 GSM8147869 1 Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP495323     Z_oocyte_stage_3_1_Pa.fastq fastq 2828372376.0 37215426.0 GSM8147869 r1 0:76 A:701751055;C:680571938;G:664212213;T:781698241;N:138929 76       701751055 680571938 664212213 781698241 138929 SRX23954972 SRS20755393 SRA1824599 Computational Biology, Stowers Institute for Medical Research Computational Biology, Stowers Institute for Medical Research                       B   usable mapping rate illumina nextseq unknown cdna_unspecified trueseq bulk bulk bulk   United States 2024-03-14 Multi-stage Embryo Oocyte Reproductive System
30759 30759 SRR28348925 SRX23954971 SRS20755392 SRP495323 PRJNA1088158 Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis. GSE261646 Transcriptome Analysis The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…   pubmed:39302832   Zebrafish Oocyte Stage II rep2 GSM8147868   source name:Oocyte|tissue:Oocyte|developmental stage:Stage II|genotype:AB TF and TLF|geo loc name:missing|collection date:missing Zebrafish Oocyte Stage II rep2 Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates Oocyte   Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.   tissue:Oocyte|developmental stage:Stage II|genotype:AB TF and TLF GSM8147868 GSM8147868: Zebrafish Oocyte Stage II rep2; Danio rerio; RNA Seq GSM8147868 r1 GSM8147868 1 Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP495323     Z_oocyte_stage_2_2_Pa.fastq fastq 2837652432.0 37337532.0 GSM8147868 r1 0:76 A:698931608;C:681467909;G:683751172;T:773364392;N:137351 76       698931608 681467909 683751172 773364392 137351 SRX23954971 SRS20755392 SRA1824599 Computational Biology, Stowers Institute for Medical Research Computational Biology, Stowers Institute for Medical Research                       B   usable mapping rate illumina nextseq unknown cdna_unspecified trueseq bulk bulk bulk   United States 2024-03-14 Multi-stage Embryo Oocyte Reproductive System
30760 30760 SRR28348926 SRX23954970 SRS20755391 SRP495323 PRJNA1088158 Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis. GSE261646 Transcriptome Analysis The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…   pubmed:39302832   Zebrafish Oocyte Stage II rep1 GSM8147867   source name:Oocyte|tissue:Oocyte|developmental stage:Stage II|genotype:AB TF and TLF|geo loc name:missing|collection date:missing Zebrafish Oocyte Stage II rep1 Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates Oocyte   Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.   tissue:Oocyte|developmental stage:Stage II|genotype:AB TF and TLF GSM8147867 GSM8147867: Zebrafish Oocyte Stage II rep1; Danio rerio; RNA Seq GSM8147867 r1 GSM8147867 1 Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP495323     Z_oocyte_stage_2_1_Pa.fastq fastq 3360126820.0 44212195.0 GSM8147867 r1 0:76 A:829333798;C:802089215;G:804982077;T:923557236;N:164494 76       829333798 802089215 804982077 923557236 164494 SRX23954970 SRS20755391 SRA1824599 Computational Biology, Stowers Institute for Medical Research Computational Biology, Stowers Institute for Medical Research                       B   usable mapping rate illumina nextseq unknown cdna_unspecified trueseq bulk bulk bulk   United States 2024-03-14 Multi-stage Embryo Oocyte Reproductive System
30761 30761 SRR28348927 SRX23954969 SRS20755390 SRP495323 PRJNA1088158 Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis. GSE261646 Transcriptome Analysis The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…   pubmed:39302832   Zebrafish Oocyte Stage I rep2 GSM8147866   source name:Oocyte|tissue:Oocyte|developmental stage:Stage I|genotype:AB TF and TLF|geo loc name:missing|collection date:missing Zebrafish Oocyte Stage I rep2 Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates Oocyte   Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.   tissue:Oocyte|developmental stage:Stage I|genotype:AB TF and TLF GSM8147866 GSM8147866: Zebrafish Oocyte Stage I rep2; Danio rerio; RNA Seq GSM8147866 r1 GSM8147866 1 Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP495323     Z_oocyte_stage_1_2_Pa.fastq fastq 2739674220.0 36048345.0 GSM8147866 r1 0:76 A:653441701;C:681445567;G:663740568;T:740918288;N:128096 76       653441701 681445567 663740568 740918288 128096 SRX23954969 SRS20755390 SRA1824599 Computational Biology, Stowers Institute for Medical Research Computational Biology, Stowers Institute for Medical Research                       B   usable mapping rate illumina nextseq unknown cdna_unspecified trueseq bulk bulk bulk   United States 2024-03-14 Multi-stage Embryo Oocyte Reproductive System
30762 30762 SRR28348928 SRX23954968 SRS20755389 SRP495323 PRJNA1088158 Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis. GSE261646 Transcriptome Analysis The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…   pubmed:39302832   Zebrafish Oocyte Stage I rep1 GSM8147865   source name:Oocyte|tissue:Oocyte|developmental stage:Stage I|genotype:AB TF and TLF|geo loc name:missing|collection date:missing Zebrafish Oocyte Stage I rep1 Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates Oocyte   Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.   tissue:Oocyte|developmental stage:Stage I|genotype:AB TF and TLF GSM8147865 GSM8147865: Zebrafish Oocyte Stage I rep1; Danio rerio; RNA Seq GSM8147865 r1 GSM8147865 1 Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP495323     Z_oocyte_stage_1_1_Pa.fastq fastq 3348831852.0 44063577.0 GSM8147865 r1 0:76 A:815134657;C:817210346;G:809175239;T:907149915;N:161695 76       815134657 817210346 809175239 907149915 161695 SRX23954968 SRS20755389 SRA1824599 Computational Biology, Stowers Institute for Medical Research Computational Biology, Stowers Institute for Medical Research                       B   usable mapping rate illumina nextseq unknown cdna_unspecified trueseq bulk bulk bulk   United States 2024-03-14 Multi-stage Embryo Oocyte Reproductive System
36273 36273 SRR298566 SRX079844 SRS212650 SRP007331 PRJNA141525 Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish. GSE29418 Transcriptome Analysis RNA libraries from immunoprecipitates of Tdrd1 Ziwi and Zili total testis RNA total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.   pubmed:21743441   WTTESTIS GSM727523   tissue:adult testis extract|strain:TL WTTESTIS three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9. adult testis extract   Tissue was homogenized in trizol and total RNA was isolated. RNAs ranging from 18 35 nucleotides were size selected from gel. For cDNA synthesis the RNA molecules in the immunoprecipitated fraction were first poly A tailed using polyApolymerase followed by ligation of synthetic RNA adapter to the five prime phosphate. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.   strain:TL GSM727523 GSM727523: WTTESTIS GSM727523: WTTESTIS GSM727523: WTTESTIS 1   GEO Accession:GSM727523 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP007331   read name barcode proc directive:ignore WTTESTIS.fastq fastq 732997980.0 20361055.0 GSM727523 1 0:36   36                 SRX079844 SRS212650 SRA039167 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.08155   0.07176   0.97851   0.52359   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2011-05-20 Adult Adult Gonad Reproductive System
36274 36274 SRR298565 SRX079843 SRS212649 SRP007331 PRJNA141525 Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish. GSE29418 Transcriptome Analysis RNA libraries from immunoprecipitates of Tdrd1 Ziwi and Zili total testis RNA total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.   pubmed:21743441   WT3WK GSM727522   tissue:3 wpf whole gonads|strain:TL WT3WK three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9. 3 wpf whole gonads   Tissue was homogenized in trizol and total RNA was isolated. RNAs ranging from 18 35 nucleotides were size selected from gel. For cDNA synthesis the RNA molecules in the immunoprecipitated fraction were first poly A tailed using polyApolymerase followed by ligation of synthetic RNA adapter to the five prime phosphate. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.   strain:TL GSM727522 GSM727522: WT3WK GSM727522: WT3WK GSM727522: WT3WK 1   GEO Accession:GSM727522 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP007331   read name barcode proc directive:ignore WT3WK.fastq fastq 365473116.0 10152031.0 GSM727522 1 0:36   36                 SRX079843 SRS212649 SRA039167 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.09055   0.0603   0.97798   0.44571   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2011-05-20 Larval Larval Gonad Reproductive System
36275 36275 SRR298564 SRX079842 SRS212648 SRP007331 PRJNA141525 Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish. GSE29418 Transcriptome Analysis RNA libraries from immunoprecipitates of Tdrd1 Ziwi and Zili total testis RNA total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.   pubmed:21743441   TDRD1WK3 GSM727521   tissue:3 wpf tdrd1 mutant gonads|strain:TL TDRD1WK3 three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9. 3 wpf tdrd1 mutant gonads   Tissue was homogenized in trizol and total RNA was isolated. RNAs ranging from 18 35 nucleotides were size selected from gel. For cDNA synthesis the RNA molecules in the immunoprecipitated fraction were first poly A tailed using polyApolymerase followed by ligation of synthetic RNA adapter to the five prime phosphate. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.   strain:TL GSM727521 GSM727521: TDRD1WK3 GSM727521: TDRD1WK3 GSM727521: TDRD1WK3 1   GEO Accession:GSM727521 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP007331   read name barcode proc directive:ignore TDRD1WK3.fastq fastq 369931536.0 10275876.0 GSM727521 1 0:36   36                 SRX079842 SRS212648 SRA039167 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.08303   0.04674   0.97938   0.35673   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2011-05-20 Larval Larval 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
36288 36288 SRR363982 SRX105295 SRS270138 SRP009275 PRJNA148581 Hen1 analysis in zebrafish GSE33582 Transcriptome Analysis small RNA libraries from wild type and Hen1 mutant testes were made with either polyA tailing VASAGFPHen1minus/plus or adapter ligation Hen1Testis and WTTestis and sequenced on an Illumina GAII platform. Overall design: RNA was isolated from total testis tissue of both Hen1 wildtype and Hen1 mutant animals. post size selection from gel the small RNA libraries wre made.   pubmed:20859253   hen1 mutant polyA GSM830244   source name:testis|strain:TL|genotype/variation:Hen1 mutant|tissue:testis|small rna library prep method:polyA tailing hen1 mutant polyA three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the zebrafish genome Zv8 testis   Small RNAs in the size range of 19 31 bases were excised from a denaturing gel. RNA was polyA tailed using polyA polymerase followed by ligation of a RNA adaptor to the five prime phosphate of the small RNAs. First strand cDNA synthesis was performed using an oligodT linker primer and M MLV RNase H reverse transcriptase. post amplification the cDNA was sent for sequencing on an Illumina/Solexa platform.   strain:TL|genotype/variation:Hen1 mutant|tissue:testis|small rna library prep method:polyA tailing GSM830244 GSM830244: hen1 mutant polyA GSM830244: hen1 mutant polyA GSM830244: hen1 mutant polyA 1   GEO Accession:GSM830244 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>44</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP009275   read name barcode proc directive:ignore VASAGFPHEN1minusMALE.fastq fastq 267208964.0 6072931.0 GSM830244 1 0:44 A:143478691;C:30051676;G:33682677;T:59883224;N:112696 44       143478691 30051676 33682677 59883224 112696 SRX105295 SRS270138 SRA047996 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.01616   0.01033   0.99381   0.76337   44   B   usable mapping rate illumina early_illumina unknown poly_a unknown bulk unknown unknown   Netherlands 2011-11-09 Undetermined Undetermined Gonad Reproductive System
36361 36361 SRR489488 SRX143565 SRS310286 SRP012376 PRJNA160143 Extensive alternative polyadenylation during zebrafish development GSE37453 Transcriptome Analysis The post transcriptional fate of messenger RNAs mRNAs is largely dictated by their three prime' untranslated regions three prime'UTRs which are defined by cleavage and polyadenylation CPA of pre mRNAs. We used polyA position profiling by sequencing 3P Seq to map polyA sites at eight developmental stages and tissues in the zebrafish. Analysis of over 60 million 3P Seq reads substantially increased and improved existing three prime'UTR annotations resulting in confidently identified three prime'UTRs for more than 78.79% of the annotated protein coding genes in zebrafish. Most zebrafish genes undergo alternative CPA with more than a thousand genes using different dominant three prime'UTRs at different stages. three prime'UTRs tend to be shortest in the ovaries and longest in the brain. Isoforms with some of the shortest three prime'UTRs are highly expressed in the ovary yet absent in the maternally contributed RNAs of the embryo perhaps because their three prime'UTRs are too short to accommodate a uridine rich motif required for stability of the maternal mRNA. At two hpf thousands of unique polyA sites appear at locations lacking a typical polyadenylation signal which suggests a wave of widespread cytoplasmic polyadenylation of mRNA degradation intermediates. Our insights into the identities formation and evolution of zebrafish three prime'UTRs provide a resource for studying gene regulation during vertebrate development. Overall design: 3P Seq was used to map the three prime' ends of protein coding genes in the zebrafish genome   pubmed:22722342   3P Seq Testis GSM919971   source name:male adults|genotype/variation:wild type|tissue:testis|development stage:adult 3P Seq Testis For 3P Seq: Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. The BED file is as in Jan et al. GSE24924 For 3P PE Seq: In each read pair read #1 captured the three prime end of the polyA tail in the antisense orientation and read #2 captured a portion of the three prime region of the transcript and occasionally the beginning of the polyA tail in the sense orientation. Read #2 began with an adapter of 26 bases. Reads with more than 10 mismatches to the adapter were discarded and the first 26 bases were removed before further processing. A read pair was considered informative only if read #1 began with Ts and read #2 contained 2–39 terminal As. post leading Ts and terminal As were removed from reads #1 and #2 respectively they were mapped to the genome using Bowtie allowing for up to two mismatches and requiring a unique mapping position in the zebrafish genome. The length of the tail encoded in read #2 was defined as the maximum number of trailing As allowing for up to one mismatch. Only cases in which this number was larger than the number of As encoded in the genome at the predicted cleavage position by at least 2 bases were carried forward. Cleavage and polyadenylation position was defined as the last non A base in read #2. The length of the polyA tail at that position was estimated using the corresponding read #1 and defined as the maximal i for which >90% of the bases in the first i bases of read #1 were Ts. This criterion was used to allow for some sequencing errors expected when sequencing long homopolymers. Genome build: danRer7 Supplementary files format and content: The .bed files contain the positions where 3P Seq reads were mapped and the name of each track is the … male adults Ovaries and testes were obtained as described in Gupta and Mullins 2010. 3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html Zebrafish embryos or adults grown under standard condition genotype/variation:wild type|tissue:testis|developmental stage:adult GSM919971 GSM919971: 3P Seq Testis; Danio rerio; RNA Seq GSM919971 1 GSM919971: 3P Seq Testis 1   GEO Accession:GSM919971 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP012376     3P_Seq_Testis.fastq fastq 633839040.0 17606640.0 GSM919971 r1 0:36 A:250493743;C:111846021;G:97558731;T:173764035;N:176510 36       250493743 111846021 97558731 173764035 176510 SRX143565 SRS310286 SRA051955 GEO Whitehead Institute for Biomedical Research 1 0.56499   0.1059   0.72468   0.46158   36   B   usable mapping rate illumina early_illumina 3prime cdna_unspecified unknown bulk unknown unknown   United States 2012-04-20 Adult Adult Gonad Reproductive System
36362 36362 SRR489487 SRX143564 SRS310285 SRP012376 PRJNA160143 Extensive alternative polyadenylation during zebrafish development GSE37453 Transcriptome Analysis The post transcriptional fate of messenger RNAs mRNAs is largely dictated by their three prime' untranslated regions three prime'UTRs which are defined by cleavage and polyadenylation CPA of pre mRNAs. We used polyA position profiling by sequencing 3P Seq to map polyA sites at eight developmental stages and tissues in the zebrafish. Analysis of over 60 million 3P Seq reads substantially increased and improved existing three prime'UTR annotations resulting in confidently identified three prime'UTRs for more than 78.79% of the annotated protein coding genes in zebrafish. Most zebrafish genes undergo alternative CPA with more than a thousand genes using different dominant three prime'UTRs at different stages. three prime'UTRs tend to be shortest in the ovaries and longest in the brain. Isoforms with some of the shortest three prime'UTRs are highly expressed in the ovary yet absent in the maternally contributed RNAs of the embryo perhaps because their three prime'UTRs are too short to accommodate a uridine rich motif required for stability of the maternal mRNA. At two hpf thousands of unique polyA sites appear at locations lacking a typical polyadenylation signal which suggests a wave of widespread cytoplasmic polyadenylation of mRNA degradation intermediates. Our insights into the identities formation and evolution of zebrafish three prime'UTRs provide a resource for studying gene regulation during vertebrate development. Overall design: 3P Seq was used to map the three prime' ends of protein coding genes in the zebrafish genome   pubmed:22722342   3P Seq Ovary GSM919970   source name:female adults|genotype/variation:wild type|tissue:ovary|development stage:adult 3P Seq Ovary For 3P Seq: Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. The BED file is as in Jan et al. GSE24924 For 3P PE Seq: In each read pair read #1 captured the three prime end of the polyA tail in the antisense orientation and read #2 captured a portion of the three prime region of the transcript and occasionally the beginning of the polyA tail in the sense orientation. Read #2 began with an adapter of 26 bases. Reads with more than 10 mismatches to the adapter were discarded and the first 26 bases were removed before further processing. A read pair was considered informative only if read #1 began with Ts and read #2 contained 2–39 terminal As. post leading Ts and terminal As were removed from reads #1 and #2 respectively they were mapped to the genome using Bowtie allowing for up to two mismatches and requiring a unique mapping position in the zebrafish genome. The length of the tail encoded in read #2 was defined as the maximum number of trailing As allowing for up to one mismatch. Only cases in which this number was larger than the number of As encoded in the genome at the predicted cleavage position by at least 2 bases were carried forward. Cleavage and polyadenylation position was defined as the last non A base in read #2. The length of the polyA tail at that position was estimated using the corresponding read #1 and defined as the maximal i for which >90% of the bases in the first i bases of read #1 were Ts. This criterion was used to allow for some sequencing errors expected when sequencing long homopolymers. Genome build: danRer7 Supplementary files format and content: The .bed files contain the positions where 3P Seq reads were mapped and the name of each track is the … female adults Ovaries and testes were obtained as described in Gupta and Mullins 2010. 3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html Zebrafish embryos or adults grown under standard condition genotype/variation:wild type|tissue:ovary|developmental stage:adult GSM919970 GSM919970: 3P Seq Ovary; Danio rerio; RNA Seq GSM919970 1 GSM919970: 3P Seq Ovary 1   GEO Accession:GSM919970 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP012376     3P_Seq_Ovary.fastq fastq 644470380.0 17901955.0 GSM919970 r1 0:36 A:263871252;C:97757369;G:94972134;T:187683515;N:186110 36       263871252 97757369 94972134 187683515 186110 SRX143564 SRS310285 SRA051955 GEO Whitehead Institute for Biomedical Research 1 0.51356   0.04868   0.821   0.48788   36   B   usable mapping rate illumina early_illumina 3prime cdna_unspecified unknown bulk unknown unknown   United States 2012-04-20 Adult Adult Gonad Reproductive System
36424 36424 SRR516545 SRX156307 SRS347187 SRP013950 PRJNA169500 Danio rerio embryonic promoterome PRJNA169500 Transcriptome Analysis Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.   pubmed:24531765 Zebrafish wild type AB strain unfertilized egg D. rerio unfertilized egg D. rerio unfertilized egg                     CAGE D. rerio unfertilized egg CAGE D. rerio unfertilized egg run2 D. rerio unfertilized egg 1     OTHER TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013950         115273233.0 4269379.0 CAGE D. rerio unfertilized egg run1 0:27 A:29909511;C:24823784;G:32519899;T:28020039;N:0 27       29909511 24823784 32519899 28020039 0 SRX156307 SRS347187 SRA055273 University of Bergen ZEPROME consortium 1 0.49872   0.07655   0.81673   0.80445   27   B   usable mapping rate illumina early_illumina unknown cage unknown bulk unknown unknown   Unknown 2012-06-28 Zygote Embryo Oocyte Reproductive System
36425 36425 SRR516546 SRX156307 SRS347187 SRP013950 PRJNA169500 Danio rerio embryonic promoterome PRJNA169500 Transcriptome Analysis Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.   pubmed:24531765 Zebrafish wild type AB strain unfertilized egg D. rerio unfertilized egg D. rerio unfertilized egg                     CAGE D. rerio unfertilized egg CAGE D. rerio unfertilized egg run2 D. rerio unfertilized egg 1     OTHER TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013950         112673943.0 4173109.0 CAGE D. rerio unfertilized egg run2 0:27 A:28315221;C:24199098;G:32599482;T:27560142;N:0 27       28315221 24199098 32599482 27560142 0 SRX156307 SRS347187 SRA055273 University of Bergen ZEPROME consortium 1 0.46201   0.06422   0.82118   0.82184   27   B   usable mapping rate illumina early_illumina unknown cage unknown bulk unknown unknown   Unknown 2012-06-28 Zygote Embryo Oocyte Reproductive System
36514 36514 SRR578923 SRX190981 SRS366702 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   SJD male GSM1014087   source name:Testes|sex:male|strain:SJD|development stage:Adult|tissue:Testes SJD male Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Testes   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:male|strain:SJD|developmental stage:Adult|tissue:Testes GSM1014087 GSM1014087: SJD male; Danio rerio; RNA Seq GSM1014087 1   1   GEO Accession:GSM1014087 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982     SJD_Male.fastq fastq 869956128.0 24165448.0 GSM1014087 r1 0:36 A:216078167;C:187750746;G:231408128;T:234642875;N:76212 36       216078167 187750746 231408128 234642875 76212 SRX190981 SRS366702 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.27444   0.19385   0.92478   0.49214   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36515 36515 SRR578922 SRX190980 SRS366701 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   Tu Male GSM1014086   source name:Testes|sex:male|strain:Tu|development stage:Adult|tissue:Testes Tu Male Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Testes   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:male|strain:Tu|developmental stage:Adult|tissue:Testes GSM1014086 GSM1014086: Tu Male; Danio rerio; RNA Seq GSM1014086 1   1   GEO Accession:GSM1014086 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982         908421696.0 25233936.0 GSM1014086 r1 0:36 A:222765185;C:198165182;G:240641436;T:246807325;N:42568 36       222765185 198165182 240641436 246807325 42568 SRX190980 SRS366701 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.1451   0.10199   0.95128   0.45517   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36516 36516 SRR578921 SRX190979 SRS366700 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   TuxSJDF2 Individual 2 GSM1014085   source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary TuxSJDF2 Individual 2 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary GSM1014085 GSM1014085: TuxSJDF2 Individual 2; Danio rerio; RNA Seq GSM1014085 1   1   GEO Accession:GSM1014085 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982         383509188.0 10653033.0 GSM1014085 r1 0:36 A:105355133;C:85084746;G:89408418;T:103592177;N:68714 36       105355133 85084746 89408418 103592177 68714 SRX190979 SRS366700 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.14582   0.10997   0.96175   0.35151   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36517 36517 SRR578920 SRX190978 SRS366699 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   TuxSJDF2 Individual 1 GSM1014084   source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary TuxSJDF2 Individual 1 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary GSM1014084 GSM1014084: TuxSJDF2 Individual 1; Danio rerio; RNA Seq GSM1014084 1   1   GEO Accession:GSM1014084 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982     TuxSJDF1_Individual_1.fastq fastq 464899752.0 12913882.0 GSM1014084 r1 0:36 A:140830427;C:93401413;G:113254459;T:117332119;N:81334 36       140830427 93401413 113254459 117332119 81334 SRX190978 SRS366699 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.43194   0.32   0.93154   0.3438   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36518 36518 SRR578919 SRX190977 SRS366698 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   TuxSJDF2 GSM1014083   source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary TuxSJDF2 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary GSM1014083 GSM1014083: TuxSJDF2; Danio rerio; RNA Seq GSM1014083 1   1   GEO Accession:GSM1014083 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982     TuxSJDF2.fastq fastq 1036162620.0 28782295.0 GSM1014083 r1 0:36 A:268457303;C:215700792;G:273583173;T:278046713;N:374639 36       268457303 215700792 273583173 278046713 374639 SRX190977 SRS366698 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.16399   0.12914   0.9517   0.52232   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36519 36519 SRR578918 SRX190976 SRS366697 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   TuxSJDF1 Individual 2 GSM1014082   source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary TuxSJDF1 Individual 2 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary GSM1014082 GSM1014082: TuxSJDF1 Individual 2; Danio rerio; RNA Seq GSM1014082 1   1   GEO Accession:GSM1014082 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982         344764980.0 9576805.0 GSM1014082 r1 0:36 A:90252809;C:80943703;G:83338280;T:90171695;N:58493 36       90252809 80943703 83338280 90171695 58493 SRX190976 SRS366697 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.18861   0.14536   0.95335   0.54431   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36520 36520 SRR578917 SRX190975 SRS366696 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   TuxSJDF1 Individual 1 GSM1014081   source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary TuxSJDF1 Individual 1 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary GSM1014081 GSM1014081: TuxSJDF1 Individual 1; Danio rerio; RNA Seq GSM1014081 1   1   GEO Accession:GSM1014081 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982     TuxSJDF2_Individual_1.fastq fastq 373504320.0 10375120.0 GSM1014081 r1 0:36 A:96550943;C:89937876;G:87356943;T:99426239;N:232319 36       96550943 89937876 87356943 99426239 232319 SRX190975 SRS366696 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.15362   0.12272   0.95943   0.56453   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36521 36521 SRR578916 SRX190974 SRS366695 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   TuxSJDF1 GSM1014080   source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary TuxSJDF1 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary GSM1014080 GSM1014080: TuxSJDF1; Danio rerio; RNA Seq GSM1014080 1   1   GEO Accession:GSM1014080 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982     TuxSJDF1.fastq fastq 1031108904.0 28641914.0 GSM1014080 r1 0:36 A:270773113;C:213123466;G:267237418;T:279702377;N:272530 36       270773113 213123466 267237418 279702377 272530 SRX190974 SRS366695 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.15469   0.12537   0.95457   0.48819   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36522 36522 SRR578915 SRX190973 SRS366694 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   Tu P0 Individual 2 GSM1014079   source name:Ovary|sex:female|strain:Tu|development stage:Adult|tissue:Ovary Tu P0 Individual 2 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Tu|developmental stage:Adult|tissue:Ovary GSM1014079 GSM1014079: Tu P0 Individual 2; Danio rerio; RNA Seq GSM1014079 1   1   GEO Accession:GSM1014079 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982         464586408.0 12905178.0 GSM1014079 r1 0:36 A:150621423;C:99131637;G:92380585;T:122374816;N:77947 36       150621423 99131637 92380585 122374816 77947 SRX190973 SRS366694 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.0937   0.05289   0.96546   0.60026   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36523 36523 SRR578914 SRX190972 SRS366693 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   Tu P0 Individual 1 GSM1014078   source name:Ovary|sex:female|strain:Tu|development stage:Adult|tissue:Ovary Tu P0 Individual 1 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Tu|developmental stage:Adult|tissue:Ovary GSM1014078 GSM1014078: Tu P0 Individual 1; Danio rerio; RNA Seq GSM1014078 1   1   GEO Accession:GSM1014078 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982         427172796.0 11865911.0 GSM1014078 r1 0:36 A:135500495;C:91385480;G:87823245;T:112202150;N:261426 36       135500495 91385480 87823245 112202150 261426 SRX190972 SRS366693 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.1368   0.09652   0.95142   0.49555   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36524 36524 SRR578913 SRX190971 SRS366692 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   Tu P0 GSM1014077   source name:Ovary|sex:female|strain:Tu|development stage:Adult|tissue:Ovary Tu P0 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Tu|developmental stage:Adult|tissue:Ovary GSM1014077 GSM1014077: Tu P0; Danio rerio; RNA Seq GSM1014077 1   1   GEO Accession:GSM1014077 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982         967772772.0 26882577.0 GSM1014077 r1 0:36 A:227085973;C:218180545;G:249458631;T:273002038;N:45585 36       227085973 218180545 249458631 273002038 45585 SRX190971 SRS366692 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.14418   0.1135   0.95818   0.51074   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36525 36525 SRR578912 SRX190970 SRS366691 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   SJDxTuF2 Individual 2 GSM1014076   source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary SJDxTuF2 Individual 2 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary GSM1014076 GSM1014076: SJDxTuF2 Individual 2; Danio rerio; RNA Seq GSM1014076 1   1   GEO Accession:GSM1014076 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982         347475024.0 9652084.0 GSM1014076 r1 0:36 A:91189258;C:81789488;G:84551251;T:89882775;N:62252 36       91189258 81789488 84551251 89882775 62252 SRX190970 SRS366691 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.15872   0.12439   0.95848   0.56717   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36526 36526 SRR578911 SRX190969 SRS366690 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   SJDxTuF2 Individual 1 GSM1014075   source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary SJDxTuF2 Individual 1 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary GSM1014075 GSM1014075: SJDxTuF2 Individual 1; Danio rerio; RNA Seq GSM1014075 1   1   GEO Accession:GSM1014075 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982         400137228.0 11114923.0 GSM1014075 r1 0:36 A:107143937;C:91495000;G:94706504;T:106722021;N:69766 36       107143937 91495000 94706504 106722021 69766 SRX190969 SRS366690 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.15753   0.12463   0.95538   0.5649   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36527 36527 SRR578910 SRX190968 SRS366689 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   SJDxTuF2 GSM1014074   source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary SJDxTuF2 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary GSM1014074 GSM1014074: SJDxTuF2; Danio rerio; RNA Seq GSM1014074 1   1   GEO Accession:GSM1014074 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982     SJDxTuF2.fastq fastq 958492116.0 26624781.0 GSM1014074 r1 0:36 A:261275440;C:193944805;G:248348765;T:254793050;N:130056 36       261275440 193944805 248348765 254793050 130056 SRX190968 SRS366689 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.20051   0.16387   0.94653   0.53263   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36528 36528 SRR578909 SRX190967 SRS366688 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   SJDxTuF1 Individual 2 GSM1014073   source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary SJDxTuF1 Individual 2 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary GSM1014073 GSM1014073: SJDxTuF1 Individual 2; Danio rerio; RNA Seq GSM1014073 1   1   GEO Accession:GSM1014073 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982         435761532.0 12104487.0 GSM1014073 r1 0:36 A:120580697;C:105605593;G:91379055;T:117787426;N:408761 36       120580697 105605593 91379055 117787426 408761 SRX190967 SRS366688 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.07215   0.05695   0.97557   0.48838   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36529 36529 SRR578908 SRX190966 SRS366687 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   SJDxTuF1 Individual 1 GSM1014072   source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary SJDxTuF1 Individual 1 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary GSM1014072 GSM1014072: SJDxTuF1 Individual 1; Danio rerio; RNA Seq GSM1014072 1   1   GEO Accession:GSM1014072 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982         378296532.0 10508237.0 GSM1014072 r1 0:36 A:109216358;C:76585213;G:90165899;T:102085771;N:243291 36       109216358 76585213 90165899 102085771 243291 SRX190966 SRS366687 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.13684   0.10794   0.96335   0.49651   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36530 36530 SRR578907 SRX190965 SRS366686 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   SJDxTuF1 GSM1014071   source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary SJDxTuF1 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary GSM1014071 GSM1014071: SJDxTuF1; Danio rerio; RNA Seq GSM1014071 1   1   GEO Accession:GSM1014071 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982         1047688380.0 29102455.0 GSM1014071 r1 0:36 A:277032474;C:213232299;G:269309034;T:288068877;N:45696 36       277032474 213232299 269309034 288068877 45696 SRX190965 SRS366686 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.1858   0.15153   0.95006   0.51345   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36531 36531 SRR578906 SRX190964 SRS366685 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   SJD P0 Individual 2 GSM1014070   source name:Ovary|sex:female|strain:SJD|development stage:Adult|tissue:Ovary SJD P0 Individual 2 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:SJD|developmental stage:Adult|tissue:Ovary GSM1014070 GSM1014070: SJD P0 Individual 2; Danio rerio; RNA Seq GSM1014070 1   1   GEO Accession:GSM1014070 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982     SJD_P0_Individual_2.fastq fastq 392951772.0 10915327.0 GSM1014070 r1 0:36 A:126709476;C:82393458;G:82997127;T:100597122;N:254589 36       126709476 82393458 82997127 100597122 254589 SRX190964 SRS366685 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.12786   0.10199   0.95724   0.52026   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36532 36532 SRR578905 SRX190963 SRS366684 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   SJD P0 Individual 1 GSM1014069   source name:Ovary|sex:female|strain:SJD|development stage:Adult|tissue:Ovary SJD P0 Individual 1 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:SJD|developmental stage:Adult|tissue:Ovary GSM1014069 GSM1014069: SJD P0 Individual 1; Danio rerio; RNA Seq GSM1014069 1   1   GEO Accession:GSM1014069 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982     SJD_P0_Individual_1.fastq fastq 379882512.0 10552292.0 GSM1014069 r1 0:36 A:122444116;C:80302064;G:76948943;T:99839311;N:348078 36       122444116 80302064 76948943 99839311 348078 SRX190963 SRS366684 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.21364   0.16206   0.94268   0.45306   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36533 36533 SRR578904 SRX190962 SRS366683 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   SJD P0 GSM1014068   source name:Ovary|sex:female|strain:SJD|development stage:Adult|tissue:Ovary SJD P0 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:SJD|developmental stage:Adult|tissue:Ovary GSM1014068 GSM1014068: SJD P0; Danio rerio; RNA Seq GSM1014068 1   1   GEO Accession:GSM1014068 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982     SJD_P0.fastq fastq 837950832.0 23276412.0 GSM1014068 r1 0:36 A:217386642;C:179519865;G:217337232;T:223633685;N:73408 36       217386642 179519865 217337232 223633685 73408 SRX190962 SRS366683 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.26607   0.21631   0.93789   0.46928   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
37921 37921 SRR1554495 SRX685396 SRS686645 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF4Ovary1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97410|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Ovary2 ZF4Ovary2 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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> SRP039502     ZF4_Ovary_3.fq.gz fastq 1225610154.0 12134754.0 Ovary2 Run3 0:101 A:347141358;C:303255805;G:280185540;T:294456010;N:571441 101       347141358 303255805 280185540 294456010 571441 SRX685396 SRS686645 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 2e-05   1e-05   1.0       101   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37922 37922 SRR1554492 SRX685395 SRS686644 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF2Testis1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97409|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Testis2 ZF2Testis2 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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> SRP039502     ZF2_Testis_3.fq.gz fastq 1192024422.0 11802222.0 Testis2 Run3 0:101 A:373380865;C:276125943;G:251033102;T:290931637;N:552875 101       373380865 276125943 251033102 290931637 552875 SRX685395 SRS686644 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 3e-05   1e-05   0.99997   0.0   101   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37925 37925 SRR1554483 SRX685391 SRS686559 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF3Ovary1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97406|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Ovary1 ZF3Ovary2 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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> SRP039502     ZF3_Ovary_3.fq.gz fastq 347516154.0 3440754.0 Ovary1 Run3 0:101 A:107805981;C:80183725;G:73617313;T:85763181;N:145954 101       107805981 80183725 73617313 85763181 145954 SRX685391 SRS686559 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 5e-05   4e-05   1.0       101   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37926 37926 SRR1554480 SRX685390 SRS686542 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF1Testis1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97405|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Testis1 ZF1Testis2 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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> SRP039502     ZF1_Testis_3.fq.gz fastq 1184228636.0 11725036.0 Testis1 Run3 0:101 A:340636900;C:278505979;G:259975802;T:304564724;N:545231 101       340636900 278505979 259975802 304564724 545231 SRX685390 SRS686542 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 1e-05   0.0   1.0       101   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37929 37929 SRR1554493 SRX683354 SRS686645 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF4Ovary1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97410|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Ovary2 ZF4Ovary1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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> SRP039502     ZF4_Ovary_1.fq.gz fastq 476104278.0 9335378.0 Ovary2 Run1 0:51 A:111060704;C:120863975;G:129849761;T:114224677;N:105161 51       111060704 120863975 129849761 114224677 105161 SRX683354 SRS686645 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.00027   8e-05   0.99945   0.8125   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37930 37930 SRR1554494 SRX683354 SRS686645 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF4Ovary1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97410|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Ovary2 ZF4Ovary1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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> SRP039502     ZF4_Ovary_2.fq.gz fastq 561956352.0 11018752.0 Ovary2 Run2 0:51 A:129925815;C:148479658;G:148478706;T:132824290;N:2247883 51       129925815 148479658 148478706 132824290 2247883 SRX683354 SRS686645 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.00022   0.0001   0.99967   0.6875   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37931 37931 SRR1554490 SRX683353 SRS686644 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF2Testis1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97409|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Testis2 ZF2Testis1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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> SRP039502     ZF2_Testis_1.fq.gz fastq 586152231.0 11493181.0 Testis2 Run1 0:51 A:145360493;C:148943988;G:151402108;T:140286245;N:159397 51       145360493 148943988 151402108 140286245 159397 SRX683353 SRS686644 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 8e-05   2e-05   0.99985   0.57142   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37932 37932 SRR1554491 SRX683353 SRS686644 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF2Testis1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97409|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Testis2 ZF2Testis1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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> SRP039502     ZF2_Testis_2.fq.gz fastq 697016337.0 13666987.0 Testis2 Run2 0:51 A:172082858;C:184634425;G:173370430;T:163527914;N:3400710 51       172082858 184634425 173370430 163527914 3400710 SRX683353 SRS686644 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 8e-05   2e-05   0.99985   0.57142   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37937 37937 SRR1554481 SRX683080 SRS686559 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF3Ovary1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97406|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Ovary1 ZF3Ovary1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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> SRP039502     ZF3_Ovary_1.fq.gz fastq 116086965.0 2276215.0 Ovary1 Run1 0:51 A:29237121;C:30235277;G:29264328;T:27320814;N:29425 51       29237121 30235277 29264328 27320814 29425 SRX683080 SRS686559 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.00022   9e-05   0.99967   0.65   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37938 37938 SRR1554482 SRX683080 SRS686559 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF3Ovary1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97406|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Ovary1 ZF3Ovary1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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> SRP039502     ZF3_Ovary_2.fq.gz fastq 138905844.0 2723644.0 Ovary1 Run2 0:51 A:34695180;C:38015933;G:33434207;T:32057083;N:703441 51       34695180 38015933 33434207 32057083 703441 SRX683080 SRS686559 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.00016   5e-05   0.99977   0.42857   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37939 37939 SRR1554478 SRX683062 SRS686542 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF1Testis1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97405|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Testis1 ZF1Testis1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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> SRP039502     ZF1_Testis_1.fq.gz fastq 655515750.0 12853250.0 Testis1 Run1 0:51 A:152422885;C:163771947;G:179144090;T:159997538;N:179290 51       152422885 163771947 179144090 159997538 179290 SRX683062 SRS686542 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.0011   0.00053   0.99829   0.67777   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37940 37940 SRR1554479 SRX683062 SRS686542 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF1Testis1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97405|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Testis1 ZF1Testis1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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> SRP039502     ZF1_Testis_2.fq.gz fastq 777594399.0 15246949.0 Testis1 Run2 0:51 A:180116528;C:202508153;G:204833105;T:186435696;N:3700917 51       180116528 202508153 204833105 186435696 3700917 SRX683062 SRS686542 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.00073   0.00032   0.99898   0.62745   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37997 37997 SRR1265760 SRX529154 SRS598851 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Testis Replicate 3 sRNAseq GSM1376643   source name:Testis|gender:male|tissue:Testis|genetic background:Wild type Singapore strain Testis Replicate 3 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Testis N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Male|tissue:Testis|genetic background:Wild type Singapore strain GSM1376643 GSM1376643: Testis Replicate 3 sRNAseq; Danio rerio; miRNA Seq GSM1376643   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376643 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZT004_GCCAAT_L004_R1.fastq.gz fastq 1096387628.0 14426153.0 GSM1376643 r1 0:76 A:268706118;C:286539627;G:262643519;T:278353167;N:145197 76       268706118 286539627 262643519 278353167 145197 SRX529154 SRS598851 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.00659   0.00333   0.99845   0.7331   76   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Gonad Reproductive System
37998 37998 SRR1265759 SRX529153 SRS598850 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Testis Replicate 2 sRNAseq GSM1376642   source name:Testis|gender:male|tissue:Testis|genetic background:Wild type Singapore strain Testis Replicate 2 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Testis N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Male|tissue:Testis|genetic background:Wild type Singapore strain GSM1376642 GSM1376642: Testis Replicate 2 sRNAseq; Danio rerio; miRNA Seq GSM1376642   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376642 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZT003_ACAGTG_L004_R1.fastq.gz fastq 1562745896.0 20562446.0 GSM1376642 r1 0:76 A:381752411;C:387452090;G:395892335;T:397438930;N:210130 76       381752411 387452090 395892335 397438930 210130 SRX529153 SRS598850 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.01222   0.00651   0.99788   0.69591   76   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Gonad Reproductive System
37999 37999 SRR1265758 SRX529152 SRS598849 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Testis Replicate 1 sRNAseq GSM1376641   source name:Testis|gender:male|tissue:Testis|genetic background:Wild type Singapore strain Testis Replicate 1 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Testis N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Male|tissue:Testis|genetic background:Wild type Singapore strain GSM1376641 GSM1376641: Testis Replicate 1 sRNAseq; Danio rerio; miRNA Seq GSM1376641   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376641 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZT001_TGACCA_L004_R1.fastq.gz fastq 1368892316.0 18011741.0 GSM1376641 r1 0:76 A:335715713;C:358829703;G:326742789;T:347419137;N:184974 76       335715713 358829703 326742789 347419137 184974 SRX529152 SRS598849 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.00032   3e-05   0.99943   0.69387   76   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo 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");;