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646 rows where devstage_curation = "Adult" and tissue_curation = "Gonad"

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experiment.library_selection >10

technology 4

experiment.library_strategy 4

experiment.platform 3

experiment.library_source 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Gonad · 646 ✖

devstage_curation_coarse 1

devstage_curation 1

  • Adult · 646 ✖
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
4407 4407 ERR1427376 ERX1497908 ERS1183210 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#48 SAMEA4012100 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012100|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#48|broker name:ArrayExpress|common name:zebrafish|fsc:NaN|gfp:NaN|individual:2|pi:NaN|plate:7|sample name:E MTAB 4617:LCK 7#48|ssc:NaN|tissue:Testes|well:H6                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#48 LCK 7#48 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Testes:tissue|Experimental Factor: NaN:fsc|Experimental Factor: NaN:ssc|Experimental Factor: NaN:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_48_mod.bam LCK_7_48.cram bam cram     E MTAB 4617:LCK 7#48 0:125 1:125 A:84706839;C:81480882;G:75512683;T:89639016;N:40330 125 125     84706839 81480882 75512683 89639016 40330 ERX1497908   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.19405 0.19075 0.02782 0.02779 0.9795 0.98013 0.73205 0.73409 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Gonad Reproductive System
4415 4415 ERR1427368 ERX1497900 ERS1183202 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#40 SAMEA4012092 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012092|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:14Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#40|broker name:ArrayExpress|common name:zebrafish|fsc:NaN|gfp:NaN|individual:2|pi:NaN|plate:7|sample name:E MTAB 4617:LCK 7#40|ssc:NaN|tissue:Testes|well:H5                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#40 LCK 7#40 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Testes:tissue|Experimental Factor: NaN:fsc|Experimental Factor: NaN:ssc|Experimental Factor: NaN:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_40_mod.bam LCK_7_40.cram bam cram     E MTAB 4617:LCK 7#40 0:125 1:125 A:98690446;C:95653530;G:87621123;T:105368805;N:43346 125 125     98690446 95653530 87621123 105368805 43346 ERX1497900   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.20112 0.19727 0.01661 0.01621 0.9797 0.9806 0.44206 0.42908 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Gonad Reproductive System
4424 4424 ERR1427359 ERX1497891 ERS1183193 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#32 SAMEA4012083 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012083|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#32|broker name:ArrayExpress|common name:zebrafish|fsc:NaN|gfp:NaN|individual:2|pi:NaN|plate:7|sample name:E MTAB 4617:LCK 7#32|ssc:NaN|tissue:Testes|well:H4                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#32 LCK 7#32 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Testes:tissue|Experimental Factor: NaN:fsc|Experimental Factor: NaN:ssc|Experimental Factor: NaN:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_32_mod.bam LCK_7_32.cram bam cram     E MTAB 4617:LCK 7#32 0:125 1:125 A:102670073;C:105552903;G:96042262;T:111286167;N:48595 125 125     102670073 105552903 96042262 111286167 48595 ERX1497891   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.0367 0.03586 0.00293 0.00297 0.99316 0.99387 0.82316 0.80581 125 125 T T mates < 9% mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Gonad Reproductive System
4433 4433 ERR1427350 ERX1497882 ERS1183184 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#24 SAMEA4012074 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012074|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#24|broker name:ArrayExpress|common name:zebrafish|fsc:NaN|gfp:NaN|individual:2|pi:NaN|plate:7|sample name:E MTAB 4617:LCK 7#24|ssc:NaN|tissue:Testes|well:H3                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#24 LCK 7#24 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Testes:tissue|Experimental Factor: NaN:fsc|Experimental Factor: NaN:ssc|Experimental Factor: NaN:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_24_mod.bam LCK_7_24.cram bam cram     E MTAB 4617:LCK 7#24 0:125 1:125 A:97411995;C:91321821;G:84912221;T:100868660;N:45803 125 125     97411995 91321821 84912221 100868660 45803 ERX1497882   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.25757 0.25144 0.03087 0.02958 0.97642 0.97695 0.71128 0.71145 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Gonad Reproductive System
4442 4442 ERR1427341 ERX1497873 ERS1183175 ERP015799 PRJEB14175 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E-MTAB-4617 Transcriptome Analysis Transcriptome data from individual lck:GFP expressing cells isolated from adult Zebrafish spleen. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T cells and NK like and a minor one of myeloid like cells. Single cell transcriptomes are matched with FACS index sorting data GFP forward and side light scatter and dead cell staining ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2016 05 26|ArrayExpress:E MTAB 4617   Protocols: The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. LCK 7#16 SAMEA4012065 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics ENA first public:2016 12 01|ENA last update:2016 05 26|External Id:SAMEA4012065|INSDC center alias:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC center name:Ludwig Center for Cancer Research University of Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics|INSDC first public:2016 12 01T17:01:24Z|INSDC last update:2016 05 26T17:59:13Z|INSDC status:public|Submitter Id:E MTAB 4617:LCK 7#16|broker name:ArrayExpress|common name:zebrafish|fsc:NaN|gfp:NaN|individual:2|pi:NaN|plate:7|sample name:E MTAB 4617:LCK 7#16|ssc:NaN|tissue:Testes|well:H2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish E MTAB 4617:LCK 7#16 LCK 7#16 Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish The spleen from a heterozygous Tglck:EGFP or wild type fish was dissected and passed through a 40μm cell strainer using the plunger of a 1 mL syringe and cells were collected in cold 1xPBS/5% FBS. A non transgenic line was used to set up the gating and exclude autofluorescent cells. Propidium iodide PI staining was used to exclude dead cells. Individual cells were sorted using a Becton Dickinson Influx sorter with 488 and 561 nm lasers Schulte et al. 2015 and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X 100 supplemented with 1 U/uL SUPERase In RNAse inhibitor Ambion. The size granularity and level of fluorescence for each cell were simultaneously recorded. The Smart seq2 protocol Picelli et al. 2014 was used to amplify the whole transcriptome and prepare libraries. Twenty five cycles of PCR amplification were performed. Experimental Factor: Testes:tissue|Experimental Factor: NaN:fsc|Experimental Factor: NaN:ssc|Experimental Factor: NaN:gfp RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>250</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>126</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP015799 Illumina HiSeq 2500 paired end sequencing; Single cell RNA sequencing of spleen derived LCK cells from adult Zebrafish ENA FIRST PUBLIC:2016 12 01|ENA LAST UPDATE:2018 11 16 LCK_7_16_mod.bam LCK_7_16.cram bam cram     E MTAB 4617:LCK 7#16 0:125 1:125 A:81321616;C:79315899;G:72476597;T:85676964;N:38424 125 125     81321616 79315899 72476597 85676964 38424 ERX1497873   ERA631093 Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics|European Nucleotide Archive 2 0.20776 0.20306 0.02431 0.02397 0.9654 0.96621 0.66321 0.66592 125 125 B B biological fallback assumption illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Switzerland 2016-05-26 Adult Adult Gonad Reproductive System
7949 7949 ERR015566 ERX005931 ERS000090 ERP000263 PRJEB2208 Zebrafish gene three prime end pull down for genome annotation E-MTAB-308 Transcriptome Analysis         ZF ovary sample1 SAMEA708832 Wellcome Sanger Institute Alias:ZF ovary sample1|Description:RNA extracted from adult zebrafish ovary|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 02 26T10:44:13Z|INSDC last update:2018 03 08T15:24:37Z|INSDC status:public|SRA accession:ERS000090|Sample Name:ERS000090|Sex:female|Strain:Tuebingen|Title:Danio rerio                 Illumina Genome Analyzer II paired end sequencing; Zebrafish gene 3 prime end pull down for genome annotation E MTAB 308:Illumina Genome Analyzer II sequencing of adult Zebrafish ovary dpf three prime pull down paired end 250 to 300 bp insert Zebrafish adult ovary mRNA three prime end Zebrafish gene three prime end pull down for genome annotation 20 ug of total RNA was fragmented using RNA Fragmentation Reagent Ambion for 5 minutes at 70 C and ethanol precipitated with glycogen and LiCl. RNA was annealed to the oligo stBPM1polyT22 biotin GGCCAGTCCTGGAGTTTTTTTTTTTTTTTTTTTTTTVN and bound to streptavidin magnetic beads. post washing by pull down on a magnet the bound RNA was reverse transcribed with SuperScript II Invitrogen and a second strand synthesised with DNA polymerase I Promega and RNase H NEB. post further washing the double strand cDNA was released from the beads with BpmI NEB. The cDNA was recovered with the QIAgen PCR Purification Kit and made into a standard Illumina library following the manufacturer's protocol with a fragment size of 250 to 300 bp. Experimental Factor: DEVELOPMENTAL STAGE:adult|Experimental Factor: ORGANISM PART:ovary|Experimental Factor: SEX:female RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina Genome Analyzer II   ERP000263 Illumina Genome Analyzer II paired end sequencing; Zebrafish gene three prime end pull down for genome annotation ENA FIRST PUBLIC:2010 08 19|ENA LAST UPDATE:2018 11 16 3444_6.srf srf 1150193272.0 7567061.0 E MTAB 308:Illumina Genome Analyzer II sequencing of adult Zebrafish ovary dpf three prime pull down paired end 250 to 300 bp insert 0:76 1:76 A:280621121;C:291623460;G:285422205;T:273609496;N:18916990 76 76     280621121 291623460 285422205 273609496 18916990 ERX005931 ERS000090 ERA010603 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.96663 0.96605 0.0126 0.01249 0.82272 0.82548 0.45602 0.45286 76 76 B B biological fallback assumption illumina early_illumina 3prime other unknown bulk unknown unknown   United Kingdom 2010-02-26 Adult Adult Gonad Reproductive System
9357 9357 ERR2983451 ERX2986067 ERS2955655 ERP112513 PRJEB30097 RNA Seq of Danionine species E-MTAB-7476 Transcriptome Analysis Tissues specific transcriptomes of Danio rerio Danio albolineatus and Danio aesculapii Brain Liver and Gonads. ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05   Protocols: Organs were sampled and snap frozen in liquid nitrogen RNA was extracted using Trizol and standard silica membrane protocol Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers. R2wG SAMEA5147910 University of Hamburg, Institute of Zoology, Molecular Animal Physiology ENA FIRST PUBLIC:2018 12 05T17:02:27Z|ENA LAST UPDATE:2018 12 05T10:01:48Z|External Id:SAMEA5147910|INSDC center name:University of Hamburg Institute of Zoology Molecular Animal Physiology|INSDC first public:2018 12 05T17:02:27Z|INSDC last update:2018 12 05T10:01:48Z|INSDC status:public|Submitter Id:E MTAB 7476:R2wG|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|individual:2|organism part:gonad|sample name:E MTAB 7476:R2wG|scientific name:Danio rerio|sex:female|strain:tu                 Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danio9 species E MTAB 7476:R2wG p R2wG p RNA Seq of Danionine species Organs were sampled and snap frozen in liquid nitrogen RNA was extracted using Trizol and standard silica membrane protocol Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers. Experimental Factor: organism:Danio rerio|Experimental Factor: organism part:gonad RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP112513 Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danionine species ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05 FCHNW2WBBXX_L6_HKZEBodsEAAFRAAPEI-209_1.fq.gz FCHNW2WBBXX_L6_HKZEBodsEAAFRAAPEI-209_2.fq.gz fastq fastq 4276100600.0 21380503.0 E MTAB 7476:FCHNW2WBBXX L6 HKZEBodsEAAFRAAPEI 209 0:100 1:100 A:1108098396;C:1033423434;G:1019885778;T:1113782383;N:910609 100 100     1108098396 1033423434 1019885778 1113782383 910609 ERX2986067 ERS2955655 ERA1674470 University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive 2 0.9444 0.94495 0.02624 0.02606 0.74959 0.7512 0.48453 0.48539 100 100 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2018-12-05 Adult Adult Gonad Reproductive System
9359 9359 ERR2983449 ERX2986065 ERS2955653 ERP112513 PRJEB30097 RNA Seq of Danionine species E-MTAB-7476 Transcriptome Analysis Tissues specific transcriptomes of Danio rerio Danio albolineatus and Danio aesculapii Brain Liver and Gonads. ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05   Protocols: Organs were sampled and snap frozen in liquid nitrogen RNA was extracted using Trizol and standard silica membrane protocol Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers. R1wG SAMEA5147908 University of Hamburg, Institute of Zoology, Molecular Animal Physiology ENA FIRST PUBLIC:2018 12 05T17:02:27Z|ENA LAST UPDATE:2018 12 05T10:01:48Z|External Id:SAMEA5147908|INSDC center name:University of Hamburg Institute of Zoology Molecular Animal Physiology|INSDC first public:2018 12 05T17:02:27Z|INSDC last update:2018 12 05T10:01:48Z|INSDC status:public|Submitter Id:E MTAB 7476:R1wG|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|individual:1|organism part:gonad|sample name:E MTAB 7476:R1wG|scientific name:Danio rerio|sex:female|strain:tu                 Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danio9 species E MTAB 7476:R1wG p R1wG p RNA Seq of Danionine species Organs were sampled and snap frozen in liquid nitrogen RNA was extracted using Trizol and standard silica membrane protocol Library was constructed using magnetic beads dT to enrich mRNA. post fragmentation the cDNA was synthesized using the mRNA fragments as templates with random hexamer primers. Experimental Factor: organism:Danio rerio|Experimental Factor: organism part:gonad RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP112513 Illumina HiSeq 4000 paired end sequencing; RNA Seq of Danionine species ENA FIRST PUBLIC:2018 12 05|ENA LAST UPDATE:2018 12 05 FCHNW2WBBXX_L6_HKZEBodsEAAERAAPEI-208_1.fq.gz FCHNW2WBBXX_L6_HKZEBodsEAAERAAPEI-208_2.fq.gz fastq fastq 3574419200.0 17872096.0 E MTAB 7476:FCHNW2WBBXX L6 HKZEBodsEAAERAAPEI 208 0:100 1:100 A:927454175;C:863033369;G:844910972;T:938253904;N:766780 100 100     927454175 863033369 844910972 938253904 766780 ERX2986065 ERS2955653 ERA1674470 University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive University of Hamburg, Institute of Zoology, Molecular Animal Physiology|European Nucleotide Archive 2 0.93851 0.93973 0.02799 0.02809 0.72701 0.72914 0.48827 0.48841 100 100 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2018-12-05 Adult Adult Gonad Reproductive System
24582 24582 SRR25462250 SRX21195051 SRS18453977 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG HE 8mpf 3 GSM7669027   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing PG HE 8mpf 3 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ GSM7669027 GSM7669027: PG HE 8mpf 3; Danio rerio; RNA Seq GSM7669027 r1 GSM7669027 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     HE_PG_8mpf_3_S11_L003_R1_001.fastq.gz HE_PG_8mpf_3_S11_L003_R2_001.fastq.gz fastq fastq 7161373434.0 60309247.0 GSM7669027 r1 0:59.39 1:59.35 A:1783731260;C:1744025029;G:1733970346;T:1880173306;N:19473493 59 59     1783731260 1744025029 1733970346 1880173306 19473493 SRX21195051 SRS18453977     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.94187 0.94592 0.01475 0.01464 0.77447 0.77498 0.45855 0.4635 60 60 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Adult Adult Gonad Reproductive System
24583 24583 SRR25462251 SRX21195050 SRS18453976 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG HE 8mpf 2 GSM7669026   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing PG HE 8mpf 2 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ GSM7669026 GSM7669026: PG HE 8mpf 2; Danio rerio; RNA Seq GSM7669026 r1 GSM7669026 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     HE_PG_8mpf_2_S7_L003_R1_001.fastq.gz HE_PG_8mpf_2_S7_L003_R2_001.fastq.gz fastq fastq 3176994053.0 26828357.0 GSM7669026 r1 0:59.22 1:59.20 A:793619267;C:767135191;G:764404567;T:830643823;N:21191205 59 59     793619267 767135191 764404567 830643823 21191205 SRX21195050 SRS18453976     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.93822 0.94226 0.01596 0.0161 0.77684 0.77772 0.47008 0.46904 59 60 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Adult Adult Gonad Reproductive System
24584 24584 SRR25462252 SRX21195049 SRS18453975 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG HE 8mpf 1 GSM7669025   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing PG HE 8mpf 1 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ GSM7669025 GSM7669025: PG HE 8mpf 1; Danio rerio; RNA Seq GSM7669025 r1 GSM7669025 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     HE_PG_8mpf_1_S6_L003_R1_001.fastq.gz HE_PG_8mpf_1_S6_L003_R2_001.fastq.gz fastq fastq 4587580737.0 38590260.0 GSM7669025 r1 0:59.45 1:59.43 A:1149031944;C:1121086335;G:1106925902;T:1203970839;N:6565717 59 59     1149031944 1121086335 1106925902 1203970839 6565717 SRX21195049 SRS18453975     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.94032 0.9437 0.01481 0.01462 0.77682 0.77774 0.45843 0.4699 58 60 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Adult Adult Gonad Reproductive System
24585 24585 SRR25462253 SRX21195048 SRS18453974 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG WT 8mpf 3 GSM7669024   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing PG WT 8mpf 3 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+ GSM7669024 GSM7669024: PG WT 8mpf 3; Danio rerio; RNA Seq GSM7669024 r1 GSM7669024 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     WT_PG_8mpf_3_S8_L003_R2_001.fastq.gz WT_PG_8mpf_3_S8_L003_R1_001.fastq.gz fastq fastq 3920821867.0 33089226.0 GSM7669024 r1 0:59.26 1:59.23 A:977738236;C:951999354;G:944769809;T:1023828622;N:22485846 59 59     977738236 951999354 944769809 1023828622 22485846 SRX21195048 SRS18453974     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.94193 0.94555 0.01657 0.01646 0.76784 0.76919 0.47238 0.47016 60 60 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Adult Adult Gonad Reproductive System
24586 24586 SRR25462254 SRX21195047 SRS18453973 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG WT 8mpf 2 GSM7669023   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing PG WT 8mpf 2 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+ GSM7669023 GSM7669023: PG WT 8mpf 2; Danio rerio; RNA Seq GSM7669023 r1 GSM7669023 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     WT_PG_8mpf_2_S10_L003_R2_001.fastq.gz WT_PG_8mpf_2_S10_L003_R1_001.fastq.gz fastq fastq 4917868553.0 41430484.0 GSM7669023 r1 0:59.37 1:59.33 A:1231173294;C:1195692797;G:1182545852;T:1292018757;N:16437853 59 59     1231173294 1195692797 1182545852 1292018757 16437853 SRX21195047 SRS18453973     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.94048 0.94432 0.0178 0.0178 0.75645 0.7569 0.46332 0.46812 59 57 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Adult Adult Gonad Reproductive System
24587 24587 SRR25462255 SRX21195046 SRS18453972 SRP452270 PRJNA1000445 CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption GSE239622 Transcriptome Analysis CDKN1A plays multiple roles in distinctive biological processes such as cellular proliferation apoptosis DNA repairing and etc. In mouse Cdkn1a deficiency led to cell arrest at G1 phase and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis and to further investigate its specific role during folliculogenesis Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly Cdkn1a deficient zebrafish were embryonic lethality resulted in approximate 2% homozygous mutants in adult stage. Furthermore homozygous mutants have accelerated follicle maturation that faster than WT and were fertile at young age 2 month. However the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually the abnormal follicles were undertaken follicle degeneration resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish particular in its critical role in maintenance of normal follicle development and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+…       PG WT 8mpf 1 GSM7669022   source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing PG WT 8mpf 1 Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file follicle   TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+ GSM7669022 GSM7669022: PG WT 8mpf 1; Danio rerio; RNA Seq GSM7669022 r1 GSM7669022 1 TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP452270     WT_PG_8mpf_1_S9_L003_R1_001.fastq.gz WT_PG_8mpf_1_S9_L003_R2_001.fastq.gz fastq fastq 3375380667.0 28408784.0 GSM7669022 r1 0:59.42 1:59.40 A:842316103;C:825987175;G:818715765;T:881225528;N:7136096 59 59     842316103 825987175 818715765 881225528 7136096 SRX21195046 SRS18453972     Karp 12006A, Biology of Vascular Program, Boston Children's Hospital 2 0.94039 0.9444 0.0162 0.01617 0.7697 0.76986 0.47132 0.46938 60 60 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nebnext bulk bulk bulk   United States 2023-07-31 Adult Adult Gonad Reproductive System
26542 26542 SRR28370185 SRX23975270 SRS20773688 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         L13 2 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 27|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E27 E27 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     L13-2_1.fq.gz L13-2_2.fq.gz fastq fastq 6912432900.0 23041443.0 L13 2 1.fq.gz 0:150 1:150 A:1784119910;C:1650041348;G:1690584500;T:1787634630;N:52512 150 150     1784119910 1650041348 1690584500 1787634630 52512 SRX23975270 SRS20773688 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26543 26543 SRR28370183 SRX23975269 SRS20773687 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         L13 3 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 29|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E29 E29 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     L13-3_1.fq.gz L13-3_2.fq.gz fastq fastq 6353525700.0 21178419.0 L13 3 1.fq.gz 0:150 1:150 A:1642863679;C:1514378445;G:1549765145;T:1646469683;N:48748 150 150     1642863679 1514378445 1549765145 1646469683 48748 SRX23975269 SRS20773687 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26544 26544 SRR28370186 SRX23975268 SRS20773685 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         L13 4 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 31|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E31 E31 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     L13-4_1.fq.gz L13-4_2.fq.gz fastq fastq 6026853600.0 20089512.0 L13 4 1.fq.gz 0:150 1:150 A:1557631540;C:1437822618;G:1472097382;T:1559255786;N:46274 150 150     1557631540 1437822618 1472097382 1559255786 46274 SRX23975268 SRS20773685 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26545 26545 SRR28370187 SRX23975267 SRS20773686 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         H27 3 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 5|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E5 E5 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     H27-3_1.fq.gz H27-3_2.fq.gz fastq fastq 6437512500.0 21458375.0 H27 3 1.fq.gz 0:150 1:150 A:1664818485;C:1534913781;G:1570911516;T:1666819538;N:49180 150 150     1664818485 1534913781 1570911516 1666819538 49180 SRX23975267 SRS20773686 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26546 26546 SRR28370188 SRX23975266 SRS20773684 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         H27 4 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 7|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E7 E7 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     H27-4_1.fq.gz H27-4_2.fq.gz fastq fastq 6583604100.0 21945347.0 H27 4 1.fq.gz 0:150 1:150 A:1701207657;C:1570727535;G:1607990863;T:1703626924;N:51121 150 150     1701207657 1570727535 1607990863 1703626924 51121 SRX23975266 SRS20773684 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26547 26547 SRR28370189 SRX23975265 SRS20773683 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         M20 1 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 9|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E9 E9 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     M20-1_1.fq.gz M20-1_2.fq.gz fastq fastq 7048815900.0 23496053.0 M20 1 1.fq.gz 0:150 1:150 A:1818915133;C:1681912688;G:1724222526;T:1823711995;N:53558 150 150     1818915133 1681912688 1724222526 1823711995 53558 SRX23975265 SRS20773683 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26548 26548 SRR28370190 SRX23975264 SRS20773682 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         M22 2 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 19|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E19 E19 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     M22-2_1.fq.gz M22-2_2.fq.gz fastq fastq 6844400100.0 22814667.0 M22 2 1.fq.gz 0:150 1:150 A:1770073015;C:1631597148;G:1666105661;T:1776572883;N:51393 150 150     1770073015 1631597148 1666105661 1776572883 51393 SRX23975264 SRS20773682 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26549 26549 SRR28370191 SRX23975263 SRS20773681 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         H27 2 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 3|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E3 E3 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     H27-2_1.fq.gz H27-2_2.fq.gz fastq fastq 6803741100.0 22679137.0 H27 2 1.fq.gz 0:150 1:150 A:1759471720;C:1621328873;G:1660379342;T:1762509905;N:51260 150 150     1759471720 1621328873 1660379342 1762509905 51260 SRX23975263 SRS20773681 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26550 26550 SRR28370184 SRX23975262 SRS20773680 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         M22 3 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 21|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E21 E21 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     M22-3_1.fq.gz M22-3_2.fq.gz fastq fastq 6312346800.0 21041156.0 M22 3 1.fq.gz 0:150 1:150 A:1638152183;C:1500304435;G:1533591340;T:1640250617;N:48225 150 150     1638152183 1500304435 1533591340 1640250617 48225 SRX23975262 SRS20773680 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26551 26551 SRR28370192 SRX23975261 SRS20773679 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         M22 4 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 23|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E23 E23 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     M22-4_1.fq.gz M22-4_2.fq.gz fastq fastq 7163095500.0 23876985.0 M22 4 1.fq.gz 0:150 1:150 A:1851012240;C:1707016293;G:1748790263;T:1856222899;N:53805 150 150     1851012240 1707016293 1748790263 1856222899 53805 SRX23975261 SRS20773679 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26552 26552 SRR28370193 SRX23975260 SRS20773678 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         L13 1 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 25|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E25 E25 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     L13-1_1.fq.gz L13-1_2.fq.gz fastq fastq 6191424300.0 20638081.0 L13 1 1.fq.gz 0:150 1:150 A:1605753886;C:1471890545;G:1506901769;T:1606830995;N:47105 150 150     1605753886 1471890545 1506901769 1606830995 47105 SRX23975260 SRS20773678 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26553 26553 SRR28370194 SRX23975259 SRS20773677 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         M22 1 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 17|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E17 E17 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     M22-1_1.fq.gz M22-1_2.fq.gz fastq fastq 6102383400.0 20341278.0 M22 1 1.fq.gz 0:150 1:150 A:1577012976;C:1455984420;G:1487747979;T:1581590987;N:47038 150 150     1577012976 1455984420 1487747979 1581590987 47038 SRX23975259 SRS20773677 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26554 26554 SRR28370195 SRX23975258 SRS20773676 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         M20 4 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 15|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E15 E15 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     M20-4_1.fq.gz M20-4_2.fq.gz fastq fastq 6636566100.0 22121887.0 M20 4 1.fq.gz 0:150 1:150 A:1715667953;C:1580553403;G:1620418612;T:1719875870;N:50262 150 150     1715667953 1580553403 1620418612 1719875870 50262 SRX23975258 SRS20773676 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26555 26555 SRR28370196 SRX23975257 SRS20773675 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         M20 3 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 13|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E13 E13 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     M20-3_1.fq.gz M20-3_2.fq.gz fastq fastq 6761256900.0 22537523.0 M20 3 1.fq.gz 0:150 1:150 A:1758917520;C:1603264927;G:1642146940;T:1756875822;N:51691 150 150     1758917520 1603264927 1642146940 1756875822 51691 SRX23975257 SRS20773675 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26556 26556 SRR28370197 SRX23975256 SRS20773674 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         M20 2 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 11|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E11 E11 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     M20-2_1.fq.gz M20-2_2.fq.gz fastq fastq 6746623800.0 22488746.0 M20 2 1.fq.gz 0:150 1:150 A:1744481110;C:1606775717;G:1646048497;T:1749267538;N:50938 150 150     1744481110 1606775717 1646048497 1749267538 50938 SRX23975256 SRS20773674 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
26557 26557 SRR28370198 SRX23975255 SRS20773673 SRP496008 PRJNA1020641 Danio rerio strain:AB strain Raw sequence reads PRJNA1020641 Whole Genome Sequencing post different low temperature treatments for 14 days transcriptome sequencing was conducted on ovaries to analyze the metabolic state under low temperatures.         H27 1 1   strain:not applicable|age:7|dev stage:month|collection date:2021 08 23|geo loc name:not applicable|sex:female|tissue:ovary|replicate:replicate=biological replicate 1|BioSampleModel:Model organism or animal                 RNA seq of ovary: adult female zebrafish E1 E1 Strand specific RNA seq libraries were prepared using the VAHTS Stranded mRNA seq Library Prep Kit for Illumina v2 Vazyme Biotech China and subjected to 150bp paired end sequencing on the Illumina Novaseq 6000 platform. Trimmomatic software was employed to remove low quality reads and sequencing adapters followed by the alignment of clean reads to the zebrafish reference genome GRCz11 v106 using STAR software. Read counts for each gene were calculated using featureCounts.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP496008     H27-1_1.fq.gz H27-1_2.fq.gz fastq fastq 6713598900.0 22378663.0 H27 1 1.fq.gz 0:150 1:150 A:1734915716;C:1602520747;G:1639382442;T:1736729508;N:50487 150 150     1734915716 1602520747 1639382442 1736729508 50487 SRX23975255 SRS20773673 SRA1825755 shanghai ocean university|College of Fisheries and Life Science shanghai ocean university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-03-18 Adult Adult Gonad Reproductive System
28800 28800 SRR26744390 SRX22443207 SRS19460925 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       TL1 AWG21KI956   strain:AB wild type|age:4 mpf|collection date:2021 10 20|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal                 RNAseq of zebrafish LM LM normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     TL1_2.clean.fq.gz TL1_1.clean.fq.gz fastq fastq 5699083800.0 18996946.0 TL1 1.clean.fq.gz 0:150 1:150 A:1551237534;C:1296027828;G:1322262120;T:1529547653;N:8665 150 150     1551237534 1296027828 1322262120 1529547653 8665 SRX22443207 SRS19460925 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92378 0.91959 0.10498 0.1026 0.6299 0.64319 0.49163 0.48651 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28801 28801 SRR26744391 SRX22443206 SRS19460924 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       OL3 AWG21KN131   strain:AB wild type|age:4 mpf|collection date:2021 10 19|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 RNAseq of zebrafish LF3 LF3 normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     OL3_2.clean.fq.gz OL3_1.clean.fq.gz fastq fastq 6314250900.0 21047503.0 OL3 1.clean.fq.gz 0:150 1:150 A:1645668992;C:1501216557;G:1526087917;T:1641268461;N:8973 150 150     1645668992 1501216557 1526087917 1641268461 8973 SRX22443206 SRS19460924 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92555 0.92469 0.01845 0.01818 0.75146 0.75298 0.4697 0.47119 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28802 28802 SRR26744392 SRX22443205 SRS19460920 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       OL2 AWG21KN130   strain:AB wild type|age:4 mpf|collection date:2021 10 18|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 RNAseq of zebrafish LF2 LF2 normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     OL2_1.clean.fq.gz OL2_2.clean.fq.gz fastq fastq 5723391300.0 19077971.0 OL2 1.clean.fq.gz 0:150 1:150 A:1493997463;C:1358589750;G:1376156813;T:1494638946;N:8328 150 150     1493997463 1358589750 1376156813 1494638946 8328 SRX22443205 SRS19460920 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92147 0.92251 0.0187 0.01891 0.75077 0.75156 0.46983 0.46864 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28803 28803 SRR26744393 SRX22443204 SRS19460923 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       OL1 AWG21KI955   strain:AB wild type|age:4 mpf|collection date:2021 10 17|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 RNAseq of zebrafish LF LF normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     OL1_1.clean.fq.gz OL1_2.clean.fq.gz fastq fastq 5769588600.0 19231962.0 OL1 1.clean.fq.gz 0:150 1:150 A:1506564191;C:1368903119;G:1393174106;T:1500937757;N:9427 150 150     1506564191 1368903119 1393174106 1500937757 9427 SRX22443204 SRS19460923 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92622 0.92542 0.01753 0.01714 0.75694 0.7596 0.47038 0.46862 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28804 28804 SRR26744394 SRX22443203 SRS19460921 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       TC3 AWG21KN129   strain:AB wild type|age:4 mpf|collection date:2021 10 16|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal                 RNAseq of zebrafish CM3 CM3 normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     TC3_2.clean.fq.gz TC3_1.clean.fq.gz fastq fastq 5849082900.0 19496943.0 TC3 1.clean.fq.gz 0:150 1:150 A:1588589470;C:1336193891;G:1355933296;T:1568357820;N:8423 150 150     1588589470 1336193891 1355933296 1568357820 8423 SRX22443203 SRS19460921 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.9259 0.92501 0.09579 0.09483 0.62501 0.6266 0.49341 0.49677 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28805 28805 SRR26744395 SRX22443202 SRS19460922 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       TC2 AWG21KN128   strain:AB wild type|age:4 mpf|collection date:2021 10 15|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal                 RNAseq of zebrafish CM2 CM2 normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     TC2_2.clean.fq.gz TC2_1.clean.fq.gz fastq fastq 6060182100.0 20200607.0 TC2 1.clean.fq.gz 0:150 1:150 A:1640267244;C:1389270827;G:1407872392;T:1622763112;N:8525 150 150     1640267244 1389270827 1407872392 1622763112 8525 SRX22443202 SRS19460922 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92414 0.9235 0.0895 0.08929 0.62528 0.62682 0.48981 0.48954 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28806 28806 SRR26744396 SRX22443201 SRS19460918 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       TC1 AWG21KI954   strain:AB wild type|age:4 mpf|collection date:2021 10 14|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal                 RNAseq of zebrafish CM CM normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     TC1_1.clean.fq.gz TC1_2.clean.fq.gz fastq fastq 5990926200.0 19969754.0 TC1 1.clean.fq.gz 0:150 1:150 A:1624594580;C:1370442060;G:1389854623;T:1606025586;N:9351 150 150     1624594580 1370442060 1389854623 1606025586 9351 SRX22443201 SRS19460918 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92373 0.92279 0.09865 0.09887 0.62568 0.62889 0.49516 0.49165 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28807 28807 SRR26744397 SRX22443200 SRS19460914 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       OC3 AWG21KN127   strain:AB wild type|age:4 mpf|collection date:2021 10 13|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 RNAseq of zebrafish CF3 CF3 normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     OC3_1.clean.fq.gz OC3_2.clean.fq.gz fastq fastq 6016914600.0 20056382.0 OC3 1.clean.fq.gz 0:150 1:150 A:1568359804;C:1431107464;G:1450792678;T:1566645836;N:8818 150 150     1568359804 1431107464 1450792678 1566645836 8818 SRX22443200 SRS19460914 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92534 0.92528 0.01718 0.017 0.75201 0.753 0.47491 0.48041 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28808 28808 SRR26744398 SRX22443199 SRS19460915 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       TL3 AWG21KN137   strain:AB wild type|age:4 mpf|collection date:2021 10 28|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal                 RNAseq of zebrafish HM3 HM3 normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     TH3_1.clean.fq.gz TH3_2.clean.fq.gz fastq fastq 5656023900.0 18853413.0 TH3 1.clean.fq.gz 0:150 1:150 A:1543170407;C:1285816998;G:1307460034;T:1519567327;N:9134 150 150     1543170407 1285816998 1307460034 1519567327 9134 SRX22443199 SRS19460915 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92316 0.92166 0.10167 0.10105 0.61546 0.61712 0.482 0.4844 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28809 28809 SRR26744399 SRX22443198 SRS19460919 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       TL2 AWG21KN136   strain:AB wild type|age:4 mpf|collection date:2021 10 27|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal                 RNAseq of zebrafish HM2 HM2 normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     TH2_2.clean.fq.gz TH2_1.clean.fq.gz fastq fastq 6625748400.0 22085828.0 TH2 1.clean.fq.gz 0:150 1:150 A:1808454203;C:1505432915;G:1526482662;T:1785369099;N:9521 150 150     1808454203 1505432915 1526482662 1785369099 9521 SRX22443198 SRS19460919 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92273 0.92286 0.09974 0.09973 0.62043 0.62203 0.48636 0.48603 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28810 28810 SRR26744400 SRX22443197 SRS19460917 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       TL1 AWG21KI958   strain:AB wild type|age:4 mpf|collection date:2021 10 26|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal                 RNAseq of zebrafish HM HM normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     TH1_1.clean.fq.gz TH1_2.clean.fq.gz fastq fastq 6588309600.0 21961032.0 TH1 1.clean.fq.gz 0:150 1:150 A:1793735270;C:1500551703;G:1518029671;T:1775983548;N:9408 150 150     1793735270 1500551703 1518029671 1775983548 9408 SRX22443197 SRS19460917 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92046 0.91969 0.10181 0.10206 0.61505 0.61477 0.48395 0.48957 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28811 28811 SRR26744401 SRX22443196 SRS19460916 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       OL3 AWG21KN135   strain:AB wild type|age:4 mpf|collection date:2021 10 25|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 RNAseq of zebrafish HF3 HF3 normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     OH3_1.clean.fq.gz OH3_2.clean.fq.gz fastq fastq 5690890500.0 18969635.0 OH3 1.clean.fq.gz 0:150 1:150 A:1485585756;C:1351021989;G:1373539521;T:1480733791;N:9443 150 150     1485585756 1351021989 1373539521 1480733791 9443 SRX22443196 SRS19460916 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92616 0.9273 0.01843 0.01865 0.74793 0.74925 0.4724 0.47202 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28812 28812 SRR26744402 SRX22443195 SRS19460912 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       OL2 AWG21KN134   strain:AB wild type|age:4 mpf|collection date:2021 10 24|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 RNAseq of zebrafish HF2 HF2 normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     OH2_2.clean.fq.gz OH2_1.clean.fq.gz fastq fastq 6047756700.0 20159189.0 OH2 1.clean.fq.gz 0:150 1:150 A:1577825068;C:1435108510;G:1458998347;T:1575814993;N:9782 150 150     1577825068 1435108510 1458998347 1575814993 9782 SRX22443195 SRS19460912 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.9233 0.92363 0.01923 0.01923 0.74474 0.74686 0.46918 0.46911 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28813 28813 SRR26744403 SRX22443194 SRS19460913 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       OL1 AWG21KI957   strain:AB wild type|age:4 mpf|collection date:2021 10 23|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 RNAseq of zebrafish HF HF normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     OH1_1.clean.fq.gz OH1_2.clean.fq.gz fastq fastq 5756713800.0 19189046.0 OH1 1.clean.fq.gz 0:150 1:150 A:1501851096;C:1366577079;G:1382910165;T:1505367292;N:8168 150 150     1501851096 1366577079 1382910165 1505367292 8168 SRX22443194 SRS19460913 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92555 0.92628 0.0184 0.01828 0.74968 0.7512 0.47643 0.4776 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28814 28814 SRR26744404 SRX22443193 SRS19460908 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       TL3 AWG21KN133   strain:AB wild type|age:4 mpf|collection date:2021 10 22|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal                 RNAseq of zebrafish LM3 LM3 normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     TL3_1.clean.fq.gz TL3_2.clean.fq.gz fastq fastq 5675551800.0 18918506.0 TL3 1.clean.fq.gz 0:150 1:150 A:1544159251;C:1294658828;G:1308831043;T:1527894467;N:8211 150 150     1544159251 1294658828 1308831043 1527894467 8211 SRX22443193 SRS19460908 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92069 0.92047 0.10371 0.10354 0.62741 0.62954 0.48923 0.48839 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28815 28815 SRR26744405 SRX22443192 SRS19460909 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       TL2 AWG21KN132   strain:AB wild type|age:4 mpf|collection date:2021 10 21|geo loc name:China|sex:male|tissue:testis|BioSampleModel:Model organism or animal                 RNAseq of zebrafish LM2 LM2 normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     TL2_1.clean.fq.gz TL2_2.clean.fq.gz fastq fastq 5834343300.0 19447811.0 TL2 1.clean.fq.gz 0:150 1:150 A:1583809689;C:1333511774;G:1345919597;T:1571093925;N:8315 150 150     1583809689 1333511774 1345919597 1571093925 8315 SRX22443192 SRS19460909 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.91878 0.92054 0.10134 0.10105 0.62708 0.62759 0.48763 0.48708 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28816 28816 SRR26744406 SRX22443191 SRS19460911 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       OC2 AWG21KN126   strain:AB wild type|age:4 mpf|collection date:2021 10 12|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 RNAseq of zebrafish CF2 CF2 normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     OC2_2.clean.fq.gz OC2_1.clean.fq.gz fastq fastq 6462335700.0 21541119.0 OC2 1.clean.fq.gz 0:150 1:150 A:1684794140;C:1535771967;G:1553892063;T:1687868172;N:9358 150 150     1684794140 1535771967 1553892063 1687868172 9358 SRX22443191 SRS19460911 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92236 0.92263 0.01803 0.01777 0.74945 0.75081 0.47372 0.47191 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult Gonad Reproductive System
28817 28817 SRR26744407 SRX22443190 SRS19460907 SRP470937 PRJNA1036532 Danio rerio Raw sequence reads PRJNA1036532 Whole Genome Sequencing normal RNAseq of zebrafish       OC1 AWG21KI953   strain:AB wild type|age:4 mpf|collection date:2021 10 11|geo loc name:China|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 RNAseq of zebrafish CF CF normal RNAseq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 4000   SRP470937     OC1_1.clean.fq.gz OC1_2.clean.fq.gz fastq fastq 5719061700.0 19063539.0 OC1 1.clean.fq.gz 0:150 1:150 A:1489404392;C:1360123113;G:1386373369;T:1483151708;N:9118 150 150     1489404392 1360123113 1386373369 1483151708 9118 SRX22443190 SRS19460907 SRA1747895 Fujian Agriculture and Forestry University|College of Marine Sciences Fujian Agriculture and Forestry University 2 0.92595 0.92513 0.0166 0.0163 0.75187 0.75503 0.47431 0.47637 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2023-11-09 Adult Adult 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
29746 29746 SRR27467679 SRX23139227 SRS20090270 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           ovary BS 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|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: ovary BS rep2 EV02003 EV02003 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 PAIRED ILLUMINA NextSeq 500   SRP482074     EV02003.R1.fastq.gz EV02003.R2.fastq.gz fastq fastq 1031891720.0 3416860.0 EV02003.R1.fastq.gz 0:151 1:151 A:264464363;C:153440613;G:408557241;T:205367487;N:62016 151 151     264464363 153440613 408557241 205367487 62016 SRX23139227 SRS20090270 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 2 0.0 0.00019 0.0 0.00015 1.0 0.99993   1.0 151 151 T T mates < 9% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Adult Adult Gonad Reproductive System
29755 29755 SRR27467688 SRX23139218 SRS20090261 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           ovary DM 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|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: ovary DM rep2 EV02002 EV02002 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 PAIRED ILLUMINA NextSeq 500   SRP482074     EV02002.R1.fastq.gz EV02002.R2.fastq.gz fastq fastq 861320308.0 2852054.0 EV02002.R1.fastq.gz 0:151 1:151 A:205625519;C:162178974;G:334206312;T:159256900;N:52603 151 151     205625519 162178974 334206312 159256900 52603 SRX23139218 SRS20090261 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 2 2e-05 0.00049 0.0 0.00027 1.0 0.99947   0.44444 151 151 T T mates < 9% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Adult Adult Gonad Reproductive System
29756 29756 SRR27467689 SRX23139217 SRS20090260 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           ovary mock 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|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: ovary mock rep2 EV02001 EV02001 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 PAIRED ILLUMINA NextSeq 500   SRP482074     EV02001.R1.fastq.gz EV02001.R2.fastq.gz fastq fastq 520371066.0 1723083.0 EV02001.R1.fastq.gz 0:151 1:151 A:116107273;C:90896560;G:218652568;T:94682244;N:32421 151 151     116107273 90896560 218652568 94682244 32421 SRX23139217 SRS20090260 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 2 2e-05 0.00086 0.0 0.00078 0.99995 0.99981 0.0 0.61538 151 151 T T mates < 9% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 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
31721 31721 SRR28537217 SRX24137319 SRS20921922 SRP499426 PRJNA1095659 lsm14b ko zebrafish RNA seq PRJNA1095659 Other Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation however the specific translational regulatory mechanisms remain unclear. Here our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes which ensures that the mRNA synthesized and stored during the growth stage of oocytes is necessary for the normal growth and development of oocytes.         ko3   strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:ko biological replicate 3|BioSampleModel:Model organism or animal                 ko3 ko3 ko3 ko ovary     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP499426     ko3_1.fq.gz ko3_2.fq.gz fastq fastq 8310654000.0 27702180.0 ko3 1.fq.gz 0:150 1:150 A:2164758632;C:1964255570;G:1984514973;T:2197073890;N:50935 150 150     2164758632 1964255570 1984514973 2197073890 50935 SRX24137319 SRS20921922     Shenzhen Second People's Hospital 2 0.9472 0.94617 0.02506 0.02527 0.74286 0.74535 0.45316 0.45662 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-04-03 Adult Adult Gonad Reproductive System
31722 31722 SRR28537218 SRX24137318 SRS20921924 SRP499426 PRJNA1095659 lsm14b ko zebrafish RNA seq PRJNA1095659 Other Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation however the specific translational regulatory mechanisms remain unclear. Here our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes which ensures that the mRNA synthesized and stored during the growth stage of oocytes is necessary for the normal growth and development of oocytes.         ko2   strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:ko biological replicate 2|BioSampleModel:Model organism or animal                 ko2 ko2 ko2 ko ovary     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP499426     ko2_1.fq.gz ko2_2.fq.gz fastq fastq 8095711800.0 26985706.0 ko2 1.fq.gz 0:150 1:150 A:2117986563;C:1909094084;G:1931885806;T:2136732639;N:12708 150 150     2117986563 1909094084 1931885806 2136732639 12708 SRX24137318 SRS20921924     Shenzhen Second People's Hospital 2 0.9483 0.94443 0.02385 0.02347 0.74266 0.74686 0.45568 0.45676 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-04-03 Adult Adult Gonad Reproductive System
31723 31723 SRR28537219 SRX24137317 SRS20921925 SRP499426 PRJNA1095659 lsm14b ko zebrafish RNA seq PRJNA1095659 Other Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation however the specific translational regulatory mechanisms remain unclear. Here our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes which ensures that the mRNA synthesized and stored during the growth stage of oocytes is necessary for the normal growth and development of oocytes.         ko1   strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:ko biological replicate 1|BioSampleModel:Model organism or animal                 ko1 ko1 ko1 ko ovary     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP499426     ko1_1.fq.gz ko1_2.fq.gz fastq fastq 9904629000.0 33015430.0 ko1 1.fq.gz 0:150 1:150 A:2565332092;C:2354153391;G:2380645312;T:2604437822;N:60383 150 150     2565332092 2354153391 2380645312 2604437822 60383 SRX24137317 SRS20921925     Shenzhen Second People's Hospital 2 0.94565 0.94416 0.01943 0.01956 0.7559 0.75739 0.456 0.45903 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-04-03 Adult Adult Gonad Reproductive System
31724 31724 SRR28537220 SRX24137316 SRS20921923 SRP499426 PRJNA1095659 lsm14b ko zebrafish RNA seq PRJNA1095659 Other Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation however the specific translational regulatory mechanisms remain unclear. Here our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes which ensures that the mRNA synthesized and stored during the growth stage of oocytes is necessary for the normal growth and development of oocytes.         wt3   strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:wt biological replicate 3|BioSampleModel:Model organism or animal                 wt3 wt3 wt3 wt ovary     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP499426     wt3_1.fq.gz wt3_2.fq.gz fastq fastq 10079485500.0 33598285.0 wt3 1.fq.gz 0:150 1:150 A:2607822943;C:2396994959;G:2427407078;T:2647197813;N:62707 150 150     2607822943 2396994959 2427407078 2647197813 62707 SRX24137316 SRS20921923     Shenzhen Second People's Hospital 2 0.94735 0.94594 0.01733 0.01743 0.75635 0.75712 0.44042 0.46348 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-04-03 Adult Adult Gonad Reproductive System
31725 31725 SRR28537221 SRX24137315 SRS20921920 SRP499426 PRJNA1095659 lsm14b ko zebrafish RNA seq PRJNA1095659 Other Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation however the specific translational regulatory mechanisms remain unclear. Here our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes which ensures that the mRNA synthesized and stored during the growth stage of oocytes is necessary for the normal growth and development of oocytes.         wt2   strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:wt biological replicate 2|BioSampleModel:Model organism or animal                 wt2 wt2 wt2 wt ovary     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP499426     wt2_2.fq.gz wt2_1.fq.gz fastq fastq 8980086900.0 29933623.0 wt2 1.fq.gz 0:150 1:150 A:2333474507;C:2131182397;G:2149144543;T:2366230132;N:55321 150 150     2333474507 2131182397 2149144543 2366230132 55321 SRX24137315 SRS20921920     Shenzhen Second People's Hospital 2 0.94182 0.94004 0.0187 0.01854 0.75077 0.75132 0.46271 0.46384 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-04-03 Adult Adult Gonad Reproductive System
31726 31726 SRR28537222 SRX24137314 SRS20921921 SRP499426 PRJNA1095659 lsm14b ko zebrafish RNA seq PRJNA1095659 Other Lsm14b LSM family member 14b is a messenger ribonucleoprotein mRNP and a widely present component in eukaryotes. Lsm14b participates in oocyte development by regulating mRNA translation however the specific translational regulatory mechanisms remain unclear. Here our goals were to explore the function of Lsm14b during early oocyte development and identify specific translational regulatory mechanisms. We established female infertile lsm14b mutant zebrafish using CRISPR/Cas9. Histological examination showed that the oocyte development in the mutant zebrafish was arrested at the primary growth PG stage. The gene set enrichment analysis GSEA analysis of the transcriptome revealed that signaling pathways associated with mRNA translation suppression and mRNA polyA tail shortening were significantly downregulation in the mutant. The polyA tail length PAT assay confirmed the mRNA polyA tail length of the oocyte development related genes zar1 and figla in the mutant. Further studies have suggested that the loss of Lsm14b triggers the unfolded protein response UPR which is related to abnormal translation inhibition. Our results demonstrate that Lsm14b assists in maintaining the translation inhibited state of mRNA by regulating the length of the mRNA polyA tail in zebrafish early oocytes which ensures that the mRNA synthesized and stored during the growth stage of oocytes is necessary for the normal growth and development of oocytes.         wt1   strain:AB|age:4 mouth|dev stage:adult|collection date:2022 07|geo loc name:not collected|sex:female|tissue:ovary|replicate:wt biological replicate 1|BioSampleModel:Model organism or animal                 wt1 wt1 wt1 wt ovary     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP499426     wt1_1.fq.gz wt1_2.fq.gz fastq fastq 5436554400.0 18121848.0 wt1 1.fq.gz 0:150 1:150 A:1418897733;C:1287256771;G:1297629578;T:1432736726;N:33592 150 150     1418897733 1287256771 1297629578 1432736726 33592 SRX24137314 SRS20921921     Shenzhen Second People's Hospital 2 0.9407 0.94657 0.02199 0.02152 0.74655 0.74679 0.47086 0.47165 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-04-03 Adult Adult Gonad Reproductive System
32362 32362 SRR29157958 SRX24679082 SRS21413713 SRP509709 PRJNA1115529 Danio rerio Raw sequence reads of gonadal tissue PRJNA1115529 Whole Genome Sequencing Evaluation of gene expression changes in zebrafish gonads following a full life cycle exposure to the non steroidal anti inflammatory drug naproxen NPX in order to evaluate the main pathways affected     The current study assessed the long term effects of environmentally relevant concentrations of NPX ng/L to low g/L on zebrafish ovary Model organism or animal sample from Danio rerio Ovary NPX   strain:AB|age:4 month|dev stage:Adult|collection date:2021 03|geo loc name:Portugal: Matosinhos|sex:female|tissue:Ovary|BioSampleModel:Model organism or animal                 zebrafish ovary RNA seq from NPX Ovary NPX Ovary NPX The current study assessed the long term effects of environmentally relevant concentrations of NPX ng/L to low g/L on parental zebrafish ovary     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP509709     H4_2.fq.gz H4_1.fq.gz H3_2.fq.gz H3_1.fq.gz H2_2.fq.gz H2_1.fq.gz H1_2.fq.gz H1_1.fq.gz fastq fastq fastq fastq fastq fastq fastq fastq 37288126200.0 124293754.0 H1 1.fq.gz 0:150 1:150 A:9870906480;C:8895442858;G:8761667172;T:9759826428;N:283262 150 150     9870906480 8895442858 8761667172 9759826428 283262 SRX24679082 SRS21413713 SRA1876810 CIIMAR - Interdisciplinary Centre of Marine and Environmental Research|EDEC - Endocrine Disruptors and Emergent Contamina CIIMAR - Interdisciplinary Centre of Marine and Environmental Research 2 0.93451 0.93482 0.01992 0.01985 0.75966 0.75943 0.45469 0.4556 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Portugal 2024-05-24 Adult Adult Gonad Reproductive System
32363 32363 SRR29157959 SRX24679081 SRS21413712 SRP509709 PRJNA1115529 Danio rerio Raw sequence reads of gonadal tissue PRJNA1115529 Whole Genome Sequencing Evaluation of gene expression changes in zebrafish gonads following a full life cycle exposure to the non steroidal anti inflammatory drug naproxen NPX in order to evaluate the main pathways affected     The current study assessed the long term effects of environmentally relevant concentrations of NPX ng/L to low g/L on zebrafish ovary Model organism or animal sample from Danio rerio Ovary Ctrl   strain:AB|age:4 month|dev stage:Adult|collection date:2021 03|geo loc name:Portugal: Matosinhos|sex:female|tissue:Ovary|BioSampleModel:Model organism or animal                 zebrafish ovary RNA seq from Control Ovary CTRL Ovary CTRL The current study assessed the long term effects of environmentally relevant concentrations of NPX ng/L to low g/L on parental zebrafish ovary     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP509709     D4_2.fq.gz D4_1.fq.gz D3_2.fq.gz D3_1.fq.gz D2_2.fq.gz D2_1.fq.gz D1_2.fq.gz D1_1.fq.gz fastq fastq fastq fastq fastq fastq fastq fastq 48240351600.0 160801172.0 D1 1.fq.gz 0:150 1:150 A:12507813252;C:11711256340;G:11706267844;T:12313668932;N:1345232 150 150     12507813252 11711256340 11706267844 12313668932 1345232 SRX24679081 SRS21413712 SRA1876810 CIIMAR - Interdisciplinary Centre of Marine and Environmental Research|EDEC - Endocrine Disruptors and Emergent Contamina CIIMAR - Interdisciplinary Centre of Marine and Environmental Research 2 0.93217 0.93303 0.01595 0.01634 0.75948 0.75998 0.46158 0.46061 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Portugal 2024-05-24 Adult Adult Gonad Reproductive System
32364 32364 SRR29157960 SRX24679080 SRS21413711 SRP509709 PRJNA1115529 Danio rerio Raw sequence reads of gonadal tissue PRJNA1115529 Whole Genome Sequencing Evaluation of gene expression changes in zebrafish gonads following a full life cycle exposure to the non steroidal anti inflammatory drug naproxen NPX in order to evaluate the main pathways affected     The current study assessed the long term effects of environmentally relevant concentrations of NPX ng/L to low g/L on zebrafish testis Model organism or animal sample from Danio rerio Testis NPX   strain:AB|age:4 month|dev stage:Adult|collection date:2021 03|geo loc name:Portugal: Matosinhos|sex:male|tissue:Testis|BioSampleModel:Model organism or animal                 zebrafish testis RNA seq from NPX Testis NPX Testis NPX The current study assessed the long term effects of environmentally relevant concentrations of NPX ng/L to low g/L on parental zebrafish testis     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP509709     G4_2.fq.gz G4_1.fq.gz G3_2.fq.gz G3_1.fq.gz G2_2.fq.gz G2_1.fq.gz G1_2.fq.gz G1_1.fq.gz fastq fastq fastq fastq fastq fastq fastq fastq 48293186700.0 160977289.0 G1 1.fq.gz 0:150 1:150 A:12737664564;C:11515099418;G:11506913376;T:12532403181;N:1106161 150 150     12737664564 11515099418 11506913376 12532403181 1106161 SRX24679080 SRS21413711 SRA1876810 CIIMAR - Interdisciplinary Centre of Marine and Environmental Research|EDEC - Endocrine Disruptors and Emergent Contamina CIIMAR - Interdisciplinary Centre of Marine and Environmental Research 2 0.93531 0.93628 0.04883 0.04847 0.66707 0.66728 0.47213 0.47226 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Portugal 2024-05-24 Adult Adult Gonad Reproductive System
32365 32365 SRR29157961 SRX24679079 SRS21413710 SRP509709 PRJNA1115529 Danio rerio Raw sequence reads of gonadal tissue PRJNA1115529 Whole Genome Sequencing Evaluation of gene expression changes in zebrafish gonads following a full life cycle exposure to the non steroidal anti inflammatory drug naproxen NPX in order to evaluate the main pathways affected     The current study assessed the long term effects of environmentally relevant concentrations of NPX ng/L to low g/L on parental zebrafish testis Model organism or animal sample from Danio rerio Testis CTRL   strain:AB|age:4 month|dev stage:Adult|collection date:2021 03|geo loc name:Portugal: Matosinhos|sex:male|tissue:Testis|BioSampleModel:Model organism or animal                 zebrafish testis RNA seq from Control Testis CTRL Testis CTRL The current study assessed the long term effects of environmentally relevant concentrations of NPX ng/L to low g/L on parental zebrafish testis     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP509709     C4_2.fq.gz C4_1.fq.gz C3_2.fq.gz C3_1.fq.gz C2_2.fq.gz C2_1.fq.gz C1_2.fq.gz C1_1.fq.gz fastq fastq fastq fastq fastq fastq fastq fastq 47457731100.0 158192437.0 C1 1.fq.gz 0:150 1:150 A:12817545225;C:10993554835;G:10941137146;T:12704995076;N:498818 150 150     12817545225 10993554835 10941137146 12704995076 498818 SRX24679079 SRS21413710 SRA1876810 CIIMAR - Interdisciplinary Centre of Marine and Environmental Research|EDEC - Endocrine Disruptors and Emergent Contamina CIIMAR - Interdisciplinary Centre of Marine and Environmental Research 2 0.93023 0.9282 0.0889 0.08851 0.63106 0.63098 0.4869 0.48618 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Portugal 2024-05-24 Adult Adult Gonad Reproductive System
33631 33631 SRR30329352 SRX25789588 SRS22421035 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo27 fish4 rep2 GSM8475571   source name:Testis|tissue:Testis|age:27 month|geo loc name:missing|collection date:missing mo27 fish4 rep2 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:27 month GSM8475571 GSM8475571: mo27 fish4 rep2; Danio rerio; RNA Seq GSM8475571 r1 GSM8475571 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 23822X4_20240226_LH00227_0052_A22HJWLLT3_S8_L003_I1_001.fastq.gz 23822X4_20240226_LH00227_0052_A22HJWLLT3_S8_L003_I2_001.fastq.gz 23822X4_20240226_LH00227_0052_A22HJWLLT3_S8_L003_R1_001.fastq.gz 23822X4_20240226_LH00227_0052_A22HJWLLT3_S8_L003_R2_001.fastq.gz fastq fastq fastq fastq 62332746910.0 328067089.0 GSM8475571 r1 0:6 1:6 2:28 3:150 A:14114753316;C:10050790836;G:11058814166;T:13983250670;N:2454362 6 6 28 150 14114753316 10050790836 11058814166 13983250670 2454362 SRX25789588 SRS22421035 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.854   0.31359   0.74659   0.69085   150   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System
33632 33632 SRR30329353 SRX25789587 SRS22421034 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo27 fish4 rep1 GSM8475570   source name:Testis|tissue:Testis|age:27 month|geo loc name:missing|collection date:missing mo27 fish4 rep1 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:27 month GSM8475570 GSM8475570: mo27 fish4 rep1; Danio rerio; RNA Seq GSM8475570 r1 GSM8475570 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 23822X3_20240226_LH00227_0052_A22HJWLLT3_S7_L003_I1_001.fastq.gz 23822X3_20240226_LH00227_0052_A22HJWLLT3_S7_L003_I2_001.fastq.gz 23822X3_20240226_LH00227_0052_A22HJWLLT3_S7_L003_R1_001.fastq.gz 23822X3_20240226_LH00227_0052_A22HJWLLT3_S7_L003_R2_001.fastq.gz fastq fastq fastq fastq 68435798090.0 360188411.0 GSM8475570 r1 0:6 1:6 2:28 3:150 A:15473213482;C:11152077954;G:12263658125;T:15136431378;N:2880711 6 6 28 150 15473213482 11152077954 12263658125 15136431378 2880711 SRX25789587 SRS22421034 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.85213   0.30845   0.7543   0.68115   150   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System
33633 33633 SRR30329354 SRX25789586 SRS22421033 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo27 fish3 rep2 GSM8475569   source name:Testis|tissue:Testis|age:27 month|geo loc name:missing|collection date:missing mo27 fish3 rep2 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:27 month GSM8475569 GSM8475569: mo27 fish3 rep2; Danio rerio; RNA Seq GSM8475569 r1 GSM8475569 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 23822X2_20240226_LH00227_0052_A22HJWLLT3_S6_L003_R2_001.fastq.gz 23822X2_20240226_LH00227_0052_A22HJWLLT3_S6_L003_R1_001.fastq.gz 23822X2_20240226_LH00227_0052_A22HJWLLT3_S6_L003_I2_001.fastq.gz 23822X2_20240226_LH00227_0052_A22HJWLLT3_S6_L003_I1_001.fastq.gz fastq fastq fastq fastq 47201245520.0 248427608.0 GSM8475569 r1 0:6 1:6 2:28 3:150 A:10398745837;C:7966730578;G:8916412008;T:9980276803;N:1975974 6 6 28 150 10398745837 7966730578 8916412008 9980276803 1975974 SRX25789586 SRS22421033 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.87941   0.25226   0.76045   0.55073   150   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System
33634 33634 SRR30329357 SRX25789585 SRS22421029 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo27 fish3 rep1 GSM8475568   source name:Testis|tissue:Testis|age:27 month|geo loc name:missing|collection date:missing mo27 fish3 rep1 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:27 month GSM8475568 GSM8475568: mo27 fish3 rep1; Danio rerio; RNA Seq GSM8475568 r1 GSM8475568 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 23822X1_20240226_LH00227_0052_A22HJWLLT3_S5_L003_R2_001.fastq.gz 23822X1_20240226_LH00227_0052_A22HJWLLT3_S5_L003_R1_001.fastq.gz 23822X1_20240226_LH00227_0052_A22HJWLLT3_S5_L003_I2_001.fastq.gz 23822X1_20240226_LH00227_0052_A22HJWLLT3_S5_L003_I1_001.fastq.gz fastq fastq fastq fastq 50530978990.0 265952521.0 GSM8475568 r1 0:6 1:6 2:28 3:150 A:10826041411;C:8852230501;G:9916508585;T:10296022501;N:2075152 6 6 28 150 10826041411 8852230501 9916508585 10296022501 2075152 SRX25789585 SRS22421029 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.89468   0.23873   0.76688   0.66783   150   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System
33635 33635 SRR30329355 SRX25789584 SRS22421032 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo27 fish2 rep1 GSM8475567   source name:Testis|tissue:Testis|age:27 month|geo loc name:missing|collection date:missing mo27 fish2 rep1 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:27 month GSM8475567 GSM8475567: mo27 fish2 rep1; Danio rerio; RNA Seq GSM8475567 r1 GSM8475567 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 19226X4_211001_A00421_0374_BHMGTFDSX2_S4_L004_I1_001.fastq.gz 19226X4_211001_A00421_0374_BHMGTFDSX2_S4_L004_I2_001.fastq.gz 19226X4_211001_A00421_0374_BHMGTFDSX2_S4_L004_R1_001.fastq.gz 19226X4_211001_A00421_0374_BHMGTFDSX2_S4_L004_R2_001.fastq.gz fastq fastq fastq fastq 61159613328.0 308886936.0 GSM8475567 r1 0:10 1:10 2:28 3:150 A:13534358992;C:9743134047;G:11041233192;T:12013610107;N:704062 10 10 28 150 13534358992 9743134047 11041233192 12013610107 704062 SRX25789584 SRS22421032 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.89529   0.10879   0.74671   0.53003   150   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System
33636 33636 SRR30329356 SRX25789583 SRS22421031 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo27 fish1 rep1 GSM8475566   source name:Testis|tissue:Testis|age:27 month|geo loc name:missing|collection date:missing mo27 fish1 rep1 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:27 month GSM8475566 GSM8475566: mo27 fish1 rep1; Danio rerio; RNA Seq GSM8475566 r1 GSM8475566 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 19226X3_211001_A00421_0374_BHMGTFDSX2_S3_L004_R2_001.fastq.gz 19226X3_211001_A00421_0374_BHMGTFDSX2_S3_L004_R1_001.fastq.gz 19226X3_211001_A00421_0374_BHMGTFDSX2_S3_L004_I2_001.fastq.gz 19226X3_211001_A00421_0374_BHMGTFDSX2_S3_L004_I1_001.fastq.gz fastq fastq fastq fastq 81122109948.0 409707626.0 GSM8475566 r1 0:10 1:10 2:28 3:150 A:18515219377;C:12708263135;G:14580444363;T:15651262388;N:954637 10 10 28 150 18515219377 12708263135 14580444363 15651262388 954637 SRX25789583 SRS22421031 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.88948   0.1044   0.77571   0.55175   150   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System
33637 33637 SRR30329358 SRX25789582 SRS22421030 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo22 fish1 rep2 GSM8475565   source name:Testis|tissue:Testis|age:22 month|geo loc name:missing|collection date:missing mo22 fish1 rep2 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:22 month GSM8475565 GSM8475565: mo22 fish1 rep2; Danio rerio; RNA Seq GSM8475565 r1 GSM8475565 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 18827X3_210414_A00421_0315_BH225KDSX2_S3_L004_I1_001.fastq.gz 18827X3_210414_A00421_0315_BH225KDSX2_S3_L004_I2_001.fastq.gz 18827X3_210414_A00421_0315_BH225KDSX2_S3_L004_R1_001.fastq.gz 18827X3_210414_A00421_0315_BH225KDSX2_S3_L004_R2_001.fastq.gz fastq fastq fastq fastq 71619246666.0 361713367.0 GSM8475565 r1 0:10 1:10 2:28 3:150 A:16269086558;C:11392726801;G:12707460817;T:13887610399;N:120475 10 10 28 150 16269086558 11392726801 12707460817 13887610399 120475 SRX25789582 SRS22421030 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.91983   0.15397   0.72354   0.51746   150   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System
33638 33638 SRR30329359 SRX25789581 SRS22421026 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo22 fish1 rep1 GSM8475564   source name:Testis|tissue:Testis|age:22 month|geo loc name:missing|collection date:missing mo22 fish1 rep1 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:22 month GSM8475564 GSM8475564: mo22 fish1 rep1; Danio rerio; RNA Seq GSM8475564 r1 GSM8475564 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 18827X1_210414_A00421_0315_BH225KDSX2_S1_L004_R2_001.fastq.gz 18827X1_210414_A00421_0315_BH225KDSX2_S1_L004_R1_001.fastq.gz 18827X1_210414_A00421_0315_BH225KDSX2_S1_L004_I2_001.fastq.gz 18827X1_210414_A00421_0315_BH225KDSX2_S1_L004_I1_001.fastq.gz fastq fastq fastq fastq 75353487858.0 380573171.0 GSM8475564 r1 0:10 1:10 2:28 3:150 A:17277856526;C:11721380902;G:13064732269;T:15021876455;N:129498 10 10 28 150 17277856526 11721380902 13064732269 15021876455 129498 SRX25789581 SRS22421026 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.91525   0.16024   0.71526   0.51211   150   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System
33639 33639 SRR30329362 SRX25789580 SRS22421025 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo20 fish1 rep2 GSM8475563   source name:Testis|tissue:Testis|age:20 month|geo loc name:missing|collection date:missing mo20 fish1 rep2 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:20 month GSM8475563 GSM8475563: mo20 fish1 rep2; Danio rerio; RNA Seq GSM8475563 r1 GSM8475563 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 18827X4_210414_A00421_0315_BH225KDSX2_S4_L004_I1_001.fastq.gz 18827X4_210414_A00421_0315_BH225KDSX2_S4_L004_I2_001.fastq.gz 18827X4_210414_A00421_0315_BH225KDSX2_S4_L004_R1_001.fastq.gz 18827X4_210414_A00421_0315_BH225KDSX2_S4_L004_R2_001.fastq.gz fastq fastq fastq fastq 66564197766.0 336182817.0 GSM8475563 r1 0:10 1:10 2:28 3:150 A:15385982034;C:10396224096;G:11708098438;T:12937004162;N:113820 10 10 28 150 15385982034 10396224096 11708098438 12937004162 113820 SRX25789580 SRS22421025 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.90394   0.15438   0.73888   0.52949   150   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System
33640 33640 SRR30329360 SRX25789579 SRS22421023 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo20 fish1 rep1 GSM8475562   source name:Testis|tissue:Testis|age:20 month|geo loc name:missing|collection date:missing mo20 fish1 rep1 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:20 month GSM8475562 GSM8475562: mo20 fish1 rep1; Danio rerio; RNA Seq GSM8475562 r1 GSM8475562 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 18827X2_210414_A00421_0315_BH225KDSX2_S2_L004_R2_001.fastq.gz 18827X2_210414_A00421_0315_BH225KDSX2_S2_L004_R1_001.fastq.gz 18827X2_210414_A00421_0315_BH225KDSX2_S2_L004_I2_001.fastq.gz 18827X2_210414_A00421_0315_BH225KDSX2_S2_L004_I1_001.fastq.gz fastq fastq fastq fastq 76196757582.0 384832109.0 GSM8475562 r1 0:10 1:10 2:28 3:150 A:17603147649;C:11925253793;G:13442889985;T:14753395348;N:129575 10 10 28 150 17603147649 11925253793 13442889985 14753395348 129575 SRX25789579 SRS22421023 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.90462   0.14351   0.74513   0.52838   150   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System
33641 33641 SRR30329361 SRX25789578 SRS22421027 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo12 fish2 rep1 GSM8475561   source name:Testis|tissue:Testis|age:12 month|geo loc name:missing|collection date:missing mo12 fish2 rep1 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:12 month GSM8475561 GSM8475561: mo12 fish2 rep1; Danio rerio; RNA Seq GSM8475561 r1 GSM8475561 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 15756X4_S4_L001_I1_001.fastq.gz 15756X4_S4_L001_R1_001.fastq.gz 15756X4_S4_L001_R2_001.fastq.gz fastq fastq fastq 29487024682.0 220052423.0 GSM8475561 r1 0:8 1:26 2:100 A:6603266449;C:4452149795;G:4932656681;T:6015543518;N:1625857 8 26 100   6603266449 4452149795 4932656681 6015543518 1625857 SRX25789578 SRS22421027 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.923   0.08981   0.74446   0.49211   100   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System

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