RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

43 rows where experiment.library_selection = "Oligo-dT", experiment.platform = "ILLUMINA" and technology = "bulk"

✎ View and edit SQL

This data as json, CSV (advanced)

tissue_curation_coarse 2

tissue_curation 2

experiment.library_source 2

devstage_curation_coarse 2

devstage_curation 2

technology 1

  • bulk · 43 ✖

experiment.platform 1

  • ILLUMINA · 43 ✖

experiment.library_strategy 1

experiment.library_selection 1

  • Oligo-dT · 43 ✖

experiment.library_layout 1

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
61876 61876 SRR13039579 SRX9489632 SRS7698470 SRP292270 PRJNA677856 Investigation of myocardial retionic acid signaling during heart regeneration in zebrafish PRJNA677856 Other Retinoic acid RA signaling is required for heart regeneration in zebrafish but the mechanism of RA mediated cardiomyocyte proliferation remains unclear. To investigate the downstream mechanism of RA mediated cardiomyocyte proliferation we generated a new transgenic line in which a loxP flanked stop cassette blocks the expression of a dominant negative form of RA receptor a b actin2:LSL dn rara and crossed this strain with a cardiomyocyte specific inducible Cre driver line cmlc2:CreER. We performed ventricular resection surgery on cmlc2:CreER; b actin2:LSL dn rara fish with and without xxx inhibition and collected 3 and 7 xxx post injury hearts to compare the gene expression profile of regenerating hearts. This project contains raw sequencing data sets of these hearts that were used to identify genes of which expression is regulated by RA signaling during regeneration.         dnRAR   strain:dnRAR|dev stage:adult|sex:pooled male and female|tissue:heart|genotype:dnRAR|sample type:tissue sample|BioSampleModel:Model organism or animal                 dnRAR pos injury 7d prep2 dnRAR 7dpi .prep2 dnRAR pos 7dpi 2 Bulk RNA Seq polyA adult zebrafish hearts     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP292270   loader:fastq load.py 7dpi_dnrar_pos_2__Index_19__GTGAAA_L001_R1.fastq.gz 7dpi_dnrar_pos_2__Index_19__GTGAAA_L002_R1.fastq.gz fastq fastq 2557840958.0 25325158.0 7dpi dnrar pos 2 Index 19 GTGAAA L001 R1.fastq.gz 0:101 A:696844669;C:559430636;G:554958018;T:745798221;N:809414 101       696844669 559430636 554958018 745798221 809414 SRX9489632 SRS7698470 SRA1157756 Victor Chang Cardiac Research Institute|Genome core Victor Chang Cardiac Research Institute 1 0.94014   0.10785   0.74742   0.51709   101   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   Australia 2020-11-16 Adult Adult Heart Cardiovascular System
61877 61877 SRR13039580 SRX9489631 SRS7698470 SRP292270 PRJNA677856 Investigation of myocardial retionic acid signaling during heart regeneration in zebrafish PRJNA677856 Other Retinoic acid RA signaling is required for heart regeneration in zebrafish but the mechanism of RA mediated cardiomyocyte proliferation remains unclear. To investigate the downstream mechanism of RA mediated cardiomyocyte proliferation we generated a new transgenic line in which a loxP flanked stop cassette blocks the expression of a dominant negative form of RA receptor a b actin2:LSL dn rara and crossed this strain with a cardiomyocyte specific inducible Cre driver line cmlc2:CreER. We performed ventricular resection surgery on cmlc2:CreER; b actin2:LSL dn rara fish with and without xxx inhibition and collected 3 and 7 xxx post injury hearts to compare the gene expression profile of regenerating hearts. This project contains raw sequencing data sets of these hearts that were used to identify genes of which expression is regulated by RA signaling during regeneration.         dnRAR   strain:dnRAR|dev stage:adult|sex:pooled male and female|tissue:heart|genotype:dnRAR|sample type:tissue sample|BioSampleModel:Model organism or animal                 dnRAR pos injury 7d prep1 dnRAR 7dpi .prep1 dnRAR pos 7dpi 1 Bulk RNA Seq polyA adult zebrafish hearts     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP292270   loader:fastq load.py 7dpi_dnrar_pos_1__Index_7__CAGATC_L001_R1.fastq.gz 7dpi_dnrar_pos_1__Index_7__CAGATC_L002_R1.fastq.gz fastq fastq 3132430463.0 31014163.0 7dpi dnrar pos 1 Index 7 CAGATC L001 R1.fastq.gz 0:101 A:853203437;C:688250700;G:670822036;T:919154522;N:999768 101       853203437 688250700 670822036 919154522 999768 SRX9489631 SRS7698470 SRA1157756 Victor Chang Cardiac Research Institute|Genome core Victor Chang Cardiac Research Institute 1 0.93753   0.11165   0.74176   0.50574   101   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   Australia 2020-11-16 Adult Adult Heart Cardiovascular System
61878 61878 SRR13039581 SRX9489630 SRS7698470 SRP292270 PRJNA677856 Investigation of myocardial retionic acid signaling during heart regeneration in zebrafish PRJNA677856 Other Retinoic acid RA signaling is required for heart regeneration in zebrafish but the mechanism of RA mediated cardiomyocyte proliferation remains unclear. To investigate the downstream mechanism of RA mediated cardiomyocyte proliferation we generated a new transgenic line in which a loxP flanked stop cassette blocks the expression of a dominant negative form of RA receptor a b actin2:LSL dn rara and crossed this strain with a cardiomyocyte specific inducible Cre driver line cmlc2:CreER. We performed ventricular resection surgery on cmlc2:CreER; b actin2:LSL dn rara fish with and without xxx inhibition and collected 3 and 7 xxx post injury hearts to compare the gene expression profile of regenerating hearts. This project contains raw sequencing data sets of these hearts that were used to identify genes of which expression is regulated by RA signaling during regeneration.         dnRAR   strain:dnRAR|dev stage:adult|sex:pooled male and female|tissue:heart|genotype:dnRAR|sample type:tissue sample|BioSampleModel:Model organism or animal                 dnRAR neg injury 7d prep2 dnRAR 7dpi+.prep2 dnRAR neg 7dpi 2 Bulk RNA Seq polyA adult zebrafish hearts     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP292270   loader:fastq load.py 7dpi_dnrar_neg_2__Index_18__GTCCGC_L001_R1.fastq.gz 7dpi_dnrar_neg_2__Index_18__GTCCGC_L002_R1.fastq.gz fastq fastq 2278975009.0 22564109.0 7dpi dnrar neg 2 Index 18 GTCCGC L001 R1.fastq.gz 0:101 A:635045082;C:485137051;G:490200341;T:667872440;N:720095 101       635045082 485137051 490200341 667872440 720095 SRX9489630 SRS7698470 SRA1157756 Victor Chang Cardiac Research Institute|Genome core Victor Chang Cardiac Research Institute 1 0.9315   0.10607   0.76242   0.51855   101   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   Australia 2020-11-16 Adult Adult Heart Cardiovascular System
61879 61879 SRR13039582 SRX9489629 SRS7698470 SRP292270 PRJNA677856 Investigation of myocardial retionic acid signaling during heart regeneration in zebrafish PRJNA677856 Other Retinoic acid RA signaling is required for heart regeneration in zebrafish but the mechanism of RA mediated cardiomyocyte proliferation remains unclear. To investigate the downstream mechanism of RA mediated cardiomyocyte proliferation we generated a new transgenic line in which a loxP flanked stop cassette blocks the expression of a dominant negative form of RA receptor a b actin2:LSL dn rara and crossed this strain with a cardiomyocyte specific inducible Cre driver line cmlc2:CreER. We performed ventricular resection surgery on cmlc2:CreER; b actin2:LSL dn rara fish with and without xxx inhibition and collected 3 and 7 xxx post injury hearts to compare the gene expression profile of regenerating hearts. This project contains raw sequencing data sets of these hearts that were used to identify genes of which expression is regulated by RA signaling during regeneration.         dnRAR   strain:dnRAR|dev stage:adult|sex:pooled male and female|tissue:heart|genotype:dnRAR|sample type:tissue sample|BioSampleModel:Model organism or animal                 dnRAR neg injury 7d prep1 dnRAR 7dpi+.prep1 dnRAR neg 7dpi 1 Bulk RNA Seq polyA adult zebrafish hearts     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP292270   loader:fastq load.py 7dpi_dnrar_neg_1__Index_6__GCCAAT_L001_R1.fastq.gz 7dpi_dnrar_neg_1__Index_6__GCCAAT_L002_R1.fastq.gz fastq fastq 3098671516.0 30679916.0 7dpi dnrar neg 1 Index 6 GCCAAT L001 R1.fastq.gz 0:101 A:830708694;C:679045290;G:682829533;T:905112282;N:975717 101       830708694 679045290 682829533 905112282 975717 SRX9489629 SRS7698470 SRA1157756 Victor Chang Cardiac Research Institute|Genome core Victor Chang Cardiac Research Institute 1 0.94733   0.08928   0.76098   0.52182   101   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   Australia 2020-11-16 Adult Adult Heart Cardiovascular System
61880 61880 SRR13039583 SRX9489628 SRS7698470 SRP292270 PRJNA677856 Investigation of myocardial retionic acid signaling during heart regeneration in zebrafish PRJNA677856 Other Retinoic acid RA signaling is required for heart regeneration in zebrafish but the mechanism of RA mediated cardiomyocyte proliferation remains unclear. To investigate the downstream mechanism of RA mediated cardiomyocyte proliferation we generated a new transgenic line in which a loxP flanked stop cassette blocks the expression of a dominant negative form of RA receptor a b actin2:LSL dn rara and crossed this strain with a cardiomyocyte specific inducible Cre driver line cmlc2:CreER. We performed ventricular resection surgery on cmlc2:CreER; b actin2:LSL dn rara fish with and without xxx inhibition and collected 3 and 7 xxx post injury hearts to compare the gene expression profile of regenerating hearts. This project contains raw sequencing data sets of these hearts that were used to identify genes of which expression is regulated by RA signaling during regeneration.         dnRAR   strain:dnRAR|dev stage:adult|sex:pooled male and female|tissue:heart|genotype:dnRAR|sample type:tissue sample|BioSampleModel:Model organism or animal                 dnRAR pos injury 3d prep2 dnRAR 3dpi .prep2 dnRAR pos 3dpi 2 Bulk RNA Seq polyA adult zebrafish hearts     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP292270   loader:fastq load.py 3dpi_dnrar_pos_2__Index_16__CCGTCC_L001_R1.fastq.gz 3dpi_dnrar_pos_2__Index_16__CCGTCC_L002_R1.fastq.gz fastq fastq 2552438165.0 25271665.0 3dpi dnrar pos 2 Index 16 CCGTCC L001 R1.fastq.gz 0:101 A:699918168;C:558564687;G:551754141;T:741401221;N:799948 101       699918168 558564687 551754141 741401221 799948 SRX9489628 SRS7698470 SRA1157756 Victor Chang Cardiac Research Institute|Genome core Victor Chang Cardiac Research Institute 1 0.93698   0.1138   0.73237   0.50509   101   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   Australia 2020-11-16 Adult Adult Heart Cardiovascular System
61881 61881 SRR13039584 SRX9489627 SRS7698470 SRP292270 PRJNA677856 Investigation of myocardial retionic acid signaling during heart regeneration in zebrafish PRJNA677856 Other Retinoic acid RA signaling is required for heart regeneration in zebrafish but the mechanism of RA mediated cardiomyocyte proliferation remains unclear. To investigate the downstream mechanism of RA mediated cardiomyocyte proliferation we generated a new transgenic line in which a loxP flanked stop cassette blocks the expression of a dominant negative form of RA receptor a b actin2:LSL dn rara and crossed this strain with a cardiomyocyte specific inducible Cre driver line cmlc2:CreER. We performed ventricular resection surgery on cmlc2:CreER; b actin2:LSL dn rara fish with and without xxx inhibition and collected 3 and 7 xxx post injury hearts to compare the gene expression profile of regenerating hearts. This project contains raw sequencing data sets of these hearts that were used to identify genes of which expression is regulated by RA signaling during regeneration.         dnRAR   strain:dnRAR|dev stage:adult|sex:pooled male and female|tissue:heart|genotype:dnRAR|sample type:tissue sample|BioSampleModel:Model organism or animal                 dnRAR pos injury 3d prep1 dnRAR 3dpi .prep1 dnRAR pos 3dpi 1 Bulk RNA Seq polyA adult zebrafish hearts     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP292270   loader:fastq load.py 3dpi_dnrar_pos_1__Index_5__ACAGTG_L001_R1.fastq.gz 3dpi_dnrar_pos_1__Index_5__ACAGTG_L002_R1.fastq.gz fastq fastq 2480623226.0 24560626.0 3dpi dnrar pos 1 Index 5 ACAGTG L001 R1.fastq.gz 0:101 A:671971518;C:540664685;G:537153082;T:730048562;N:785379 101       671971518 540664685 537153082 730048562 785379 SRX9489627 SRS7698470 SRA1157756 Victor Chang Cardiac Research Institute|Genome core Victor Chang Cardiac Research Institute 1 0.94428   0.11728   0.7427   0.49988   101   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   Australia 2020-11-16 Adult Adult Heart Cardiovascular System
61882 61882 SRR13039585 SRX9489626 SRS7698470 SRP292270 PRJNA677856 Investigation of myocardial retionic acid signaling during heart regeneration in zebrafish PRJNA677856 Other Retinoic acid RA signaling is required for heart regeneration in zebrafish but the mechanism of RA mediated cardiomyocyte proliferation remains unclear. To investigate the downstream mechanism of RA mediated cardiomyocyte proliferation we generated a new transgenic line in which a loxP flanked stop cassette blocks the expression of a dominant negative form of RA receptor a b actin2:LSL dn rara and crossed this strain with a cardiomyocyte specific inducible Cre driver line cmlc2:CreER. We performed ventricular resection surgery on cmlc2:CreER; b actin2:LSL dn rara fish with and without xxx inhibition and collected 3 and 7 xxx post injury hearts to compare the gene expression profile of regenerating hearts. This project contains raw sequencing data sets of these hearts that were used to identify genes of which expression is regulated by RA signaling during regeneration.         dnRAR   strain:dnRAR|dev stage:adult|sex:pooled male and female|tissue:heart|genotype:dnRAR|sample type:tissue sample|BioSampleModel:Model organism or animal                 dnRAR neg injury 3d prep2 dnRAR 3dpi+.prep2 dnRAR neg 3dpi 2 Bulk RNA Seq polyA adult zebrafish hearts     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP292270   loader:fastq load.py 3dpi_dnrar_neg_2__Index_4__TGACCA_L001_R1.fastq.gz 3dpi_dnrar_neg_2__Index_4__TGACCA_L002_R1.fastq.gz fastq fastq 3727815060.0 36909060.0 3dpi dnrar neg 2 Index 4 TGACCA L001 R1.fastq.gz 0:101 A:1007850641;C:819931567;G:814026286;T:1084822648;N:1183918 101       1007850641 819931567 814026286 1084822648 1183918 SRX9489626 SRS7698470 SRA1157756 Victor Chang Cardiac Research Institute|Genome core Victor Chang Cardiac Research Institute 1 0.9401   0.10133   0.73411   0.50092   101   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   Australia 2020-11-16 Adult Adult Heart Cardiovascular System
61883 61883 SRR13039586 SRX9489625 SRS7698470 SRP292270 PRJNA677856 Investigation of myocardial retionic acid signaling during heart regeneration in zebrafish PRJNA677856 Other Retinoic acid RA signaling is required for heart regeneration in zebrafish but the mechanism of RA mediated cardiomyocyte proliferation remains unclear. To investigate the downstream mechanism of RA mediated cardiomyocyte proliferation we generated a new transgenic line in which a loxP flanked stop cassette blocks the expression of a dominant negative form of RA receptor a b actin2:LSL dn rara and crossed this strain with a cardiomyocyte specific inducible Cre driver line cmlc2:CreER. We performed ventricular resection surgery on cmlc2:CreER; b actin2:LSL dn rara fish with and without xxx inhibition and collected 3 and 7 xxx post injury hearts to compare the gene expression profile of regenerating hearts. This project contains raw sequencing data sets of these hearts that were used to identify genes of which expression is regulated by RA signaling during regeneration.         dnRAR   strain:dnRAR|dev stage:adult|sex:pooled male and female|tissue:heart|genotype:dnRAR|sample type:tissue sample|BioSampleModel:Model organism or animal                 dnRAR neg injury 3d prep1 dnRAR 3dpi+.prep1 dnRAR neg 3dpi 1 Bulk RNA Seq polyA adult zebrafish hearts     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP292270   loader:fastq load.py 3dpi_dnrar_neg_1__Index_15__ATGTCA_L001_R1.fastq.gz 3dpi_dnrar_neg_1__Index_15__ATGTCA_L002_R1.fastq.gz fastq fastq 2223709122.0 22016922.0 3dpi dnrar neg 1 Index 15 ATGTCA L001 R1.fastq.gz 0:101 A:611860221;C:483613969;G:480670356;T:646860324;N:704252 101       611860221 483613969 480670356 646860324 704252 SRX9489625 SRS7698470 SRA1157756 Victor Chang Cardiac Research Institute|Genome core Victor Chang Cardiac Research Institute 1 0.93682   0.10961   0.73192   0.50015   101   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   Australia 2020-11-16 Adult Adult Heart Cardiovascular System
61884 61884 SRR13039587 SRX9489624 SRS7698469 SRP292270 PRJNA677856 Investigation of myocardial retionic acid signaling during heart regeneration in zebrafish PRJNA677856 Other Retinoic acid RA signaling is required for heart regeneration in zebrafish but the mechanism of RA mediated cardiomyocyte proliferation remains unclear. To investigate the downstream mechanism of RA mediated cardiomyocyte proliferation we generated a new transgenic line in which a loxP flanked stop cassette blocks the expression of a dominant negative form of RA receptor a b actin2:LSL dn rara and crossed this strain with a cardiomyocyte specific inducible Cre driver line cmlc2:CreER. We performed ventricular resection surgery on cmlc2:CreER; b actin2:LSL dn rara fish with and without xxx inhibition and collected 3 and 7 xxx post injury hearts to compare the gene expression profile of regenerating hearts. This project contains raw sequencing data sets of these hearts that were used to identify genes of which expression is regulated by RA signaling during regeneration.         wild type   strain:EKW|dev stage:adult|sex:pooled male and female|tissue:heart|genotype:WT|sample type:tissue sample|BioSampleModel:Model organism or animal                 WT no injury prep2 WT 3dpi WT no inj 2 Bulk RNA Seq polyA adult zebrafish hearts     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP292270   loader:fastq load.py Control__Index_12__CTTGTA_L001_R1.fastq.gz Control__Index_12__CTTGTA_L002_R1.fastq.gz fastq fastq 2875406976.0 28469376.0 Control Index 12 CTTGTA L001 R1.fastq.gz 0:101 A:775335613;C:621594724;G:635510080;T:842057810;N:908749 101       775335613 621594724 635510080 842057810 908749 SRX9489624 SRS7698469 SRA1157756 Victor Chang Cardiac Research Institute|Genome core Victor Chang Cardiac Research Institute 1 0.94749   0.08801   0.76824   0.46639   101   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   Australia 2020-11-16 Adult Adult Heart Cardiovascular System
61885 61885 SRR13039588 SRX9489623 SRS7698469 SRP292270 PRJNA677856 Investigation of myocardial retionic acid signaling during heart regeneration in zebrafish PRJNA677856 Other Retinoic acid RA signaling is required for heart regeneration in zebrafish but the mechanism of RA mediated cardiomyocyte proliferation remains unclear. To investigate the downstream mechanism of RA mediated cardiomyocyte proliferation we generated a new transgenic line in which a loxP flanked stop cassette blocks the expression of a dominant negative form of RA receptor a b actin2:LSL dn rara and crossed this strain with a cardiomyocyte specific inducible Cre driver line cmlc2:CreER. We performed ventricular resection surgery on cmlc2:CreER; b actin2:LSL dn rara fish with and without xxx inhibition and collected 3 and 7 xxx post injury hearts to compare the gene expression profile of regenerating hearts. This project contains raw sequencing data sets of these hearts that were used to identify genes of which expression is regulated by RA signaling during regeneration.         wild type   strain:EKW|dev stage:adult|sex:pooled male and female|tissue:heart|genotype:WT|sample type:tissue sample|BioSampleModel:Model organism or animal                 WT no injury prep1 WT WT no inj 1 Bulk RNA Seq polyA adult zebrafish hearts     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP292270   loader:fastq load.py Control_1__Index_2__CGATGT_L001_R1.fastq.gz Control_1__Index_2__CGATGT_L002_R1.fastq.gz fastq fastq 3242985366.0 32108766.0 Control 1 Index 2 CGATGT L001 R1.fastq.gz 0:101 A:855046773;C:717010168;G:731584171;T:938335515;N:1008739 101       855046773 717010168 731584171 938335515 1008739 SRX9489623 SRS7698469 SRA1157756 Victor Chang Cardiac Research Institute|Genome core Victor Chang Cardiac Research Institute 1 0.95209   0.07554   0.77039   0.5332   101   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   Australia 2020-11-16 Adult Adult Heart Cardiovascular System
72120 72120 SRR22366730 SRX18337367 SRS15826352 SRP407292 PRJNA900299 Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration PRJNA900299 Other Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.     single cell RNA seq of macrophage and neutrophil cells sorted from 7 day post injured zebrafish heart with CL condition single cell RNA seq of macrophage and neutrophil cells sorted from 7 day post injured zebrafish heart with CL condition sc CL 7dpci   strain:wild type AB|age:3 month to 1 year old|sex:male and female|tissue:heart|cell type:macrophage and neutrophil|treatment:7day post cryoinjured heart with CL condition|BioSampleModel:Model organism or animal                 single cell RNA seq of macrophage and neutrophil cells sorted from 7 day post zebrafish injured heart in CL condition HS19157 1 HS19157 1 7 day post cryoinjured CL     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP407292     HS19157-1_S1_L001_I1_001.fastq.gz HS19157-1_S1_L001_R1_001.fastq.gz HS19157-1_S1_L001_R2_001.fastq.gz fastq fastq fastq 29030208386.0 228584318.0 HS19157 1 S1 L001 I1 001.fastq.gz 0:8 1:28 2:91 A:6001335918;C:4374546179;G:4652617189;T:5772031621;N:642031 8 28 91   6001335918 4374546179 4652617189 5772031621 642031 SRX18337367 SRS15826352 SRA1544923 Academia Sinica|Institute of Biomedical Sciences Academia Sinica 1 0.90785   0.14887   0.80955   0.54438   91   B   usable mapping rate illumina hiseq_era unknown poly_a unknown sc bulk bulk   Taiwan 2022-11-22 Adult Adult Heart Cardiovascular System
72121 72121 SRR22366731 SRX18337366 SRS15826351 SRP407292 PRJNA900299 Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration PRJNA900299 Other Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.     single cell RNA seq of macrophage and neutrophil cells sorted from 3 day post injured zebrafish heart with CL condition single cell RNA seq of macrophage and neutrophil cells sorted from 3 day post injured zebrafish heart with CL condition sc CL 3dpci   strain:wild type AB|age:3 month to 1 year old|sex:male and female|tissue:heart|cell type:macrophage and neutrophil|treatment:3day post cryoinjured heart with CL condition|BioSampleModel:Model organism or animal                 single cell RNA seq of macrophage and neutrophil cells sorted from 3 day post zebrafish injured heart in CL condition KO 10X GEX ZBNM CL KO 10X GEX ZBNM CL 3 day post cryoinjured CL     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP407292     KO_10X_GEX_ZBNM_CL_S1_L002_I1_001.fastq.gz KO_10X_GEX_ZBNM_CL_S1_L002_I2_001.fastq.gz KO_10X_GEX_ZBNM_CL_S1_L002_R1_001.fastq.gz KO_10X_GEX_ZBNM_CL_S1_L002_R2_001.fastq.gz fastq fastq fastq fastq 136386569076.0 428888582.0 KO 10X GEX ZBNM CL S1 L002 I1 001.fastq.gz 0:8 1:8 2:151 3:151 A:55416348531;C:22858620140;G:22320883224;T:28927596919;N:902950 8 8 151 151 55416348531 22858620140 22320883224 28927596919 902950 SRX18337366 SRS15826351 SRA1544923 Academia Sinica|Institute of Biomedical Sciences Academia Sinica 2 5e-05 0.91197 4e-05 0.16298 1.0 0.81531   0.6066 151 151 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc bulk bulk   Taiwan 2022-11-23 Adult Adult Heart Cardiovascular System
72122 72122 SRR22366732 SRX18337365 SRS15826349 SRP407292 PRJNA900299 Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration PRJNA900299 Other Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.     single cell RNA seq of macrophage and neutrophil cells sorted from 1 day post injured zebrafish heart with CL condition single cell RNA seq of macrophage and neutrophil cells sorted from 1 day post injured zebrafish heart with CL condition sc CL 1dpci   strain:wild type AB|age:3 month to 1 year old|sex:male and female|tissue:heart|cell type:macrophage and neutrophil|treatment:1day post cryoinjured heart with CL condition|BioSampleModel:Model organism or animal                 single cell RNA seq of macrophage and neutrophil cells sorted from 1 day post zebrafish injured heart in CL condition KO 10X GEX ZBNMCL1dpci KO 10X GEX ZBNMCL1dpci 1 day post cryoinjured CL     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP407292     KO_10X_GEX_ZBNMCL1dpci_S6_L002_R2_001.fastq.gz KO_10X_GEX_ZBNMCL1dpci_S6_L002_R1_001.fastq.gz KO_10X_GEX_ZBNMCL1dpci_S6_L002_I2_001.fastq.gz KO_10X_GEX_ZBNMCL1dpci_S6_L002_I1_001.fastq.gz fastq fastq fastq fastq 116701252260.0 366985070.0 KO 10X GEX ZBNMCL1dpci S6 L002 I1 001.fastq.gz 0:8 1:8 2:151 3:151 A:47399839020;C:19285022403;G:18825392415;T:25318468073;N:769229 8 8 151 151 47399839020 19285022403 18825392415 25318468073 769229 SRX18337365 SRS15826349 SRA1544923 Academia Sinica|Institute of Biomedical Sciences Academia Sinica 2 0.0 0.91164 0.0 0.16285 1.0 0.82132   0.60109 151 151 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc bulk bulk   Taiwan 2022-11-23 Adult Adult Heart Cardiovascular System
72123 72123 SRR22366733 SRX18337364 SRS15826350 SRP407292 PRJNA900299 Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration PRJNA900299 Other Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.     single cell RNA seq of macrophage and neutrophil cells sorted from 7 day post injured zebrafish heart with PBS condition single cell RNA seq of macrophage and neutrophil cells sorted from 7 day post injured zebrafish heart with PBS condition sc PBS 7dpci   strain:wild type AB|age:3 month to 1 year old|sex:male and female|tissue:heart|cell type:macrophage and neutrophil|treatment:7day post cryoinjured heart with PBS condition|BioSampleModel:Model organism or animal                 single cell RNA seq of macrophage and neutrophil cells sorted from 7 day post zebrafish injured heart in PBS condition HS19157 2 HS19157 2 7 day post cryoinjured PBS     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP407292     HS19157-2_S2_L001_I1_001.fastq.gz HS19157-2_S2_L001_R1_001.fastq.gz HS19157-2_S2_L001_R2_001.fastq.gz fastq fastq fastq 27285141518.0 214843634.0 HS19157 2 S2 L001 I1 001.fastq.gz 0:8 1:28 2:91 A:5601997478;C:4186239866;G:4438635185;T:5323299767;N:598398 8 28 91   5601997478 4186239866 4438635185 5323299767 598398 SRX18337364 SRS15826350 SRA1544923 Academia Sinica|Institute of Biomedical Sciences Academia Sinica 1 0.91295   0.12796   0.81917   0.54156   91   B   usable mapping rate illumina hiseq_era unknown poly_a unknown sc bulk bulk   Taiwan 2022-11-22 Adult Adult Heart Cardiovascular System
72124 72124 SRR22366734 SRX18337363 SRS15826348 SRP407292 PRJNA900299 Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration PRJNA900299 Other Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.     single cell RNA seq of macrophage and neutrophil cells sorted from 3 day post injured zebrafish heart with PBS condition single cell RNA seq of macrophage and neutrophil cells sorted from 3 day post injured zebrafish heart with PBS condition sc PBS 3dpci   strain:wild type AB|age:3 month to 1 year old|sex:male and female|tissue:heart|cell type:macrophage and neutrophil|treatment:3day post cryoinjured heart with PBS condition|BioSampleModel:Model organism or animal                 single cell RNA seq of macrophage and neutrophil cells sorted from 3 day post zebrafish injured heart in PBS condition KO 10X GEX ZBNM PBS KO 10X GEX ZBNM PBS 3 day post cryoinjured PBS     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP407292     KO_10X_GEX_ZBNM_PBS_S2_L002_I1_001.fastq.gz KO_10X_GEX_ZBNM_PBS_S2_L002_I2_001.fastq.gz KO_10X_GEX_ZBNM_PBS_S2_L002_R1_001.fastq.gz KO_10X_GEX_ZBNM_PBS_S2_L002_R2_001.fastq.gz fastq fastq fastq fastq 90678465744.0 285152408.0 KO 10X GEX ZBNM PBS S2 L002 I1 001.fastq.gz 0:8 1:8 2:151 3:151 A:36925379975;C:14988640095;G:14661131954;T:19540280259;N:594933 8 8 151 151 36925379975 14988640095 14661131954 19540280259 594933 SRX18337363 SRS15826348 SRA1544923 Academia Sinica|Institute of Biomedical Sciences Academia Sinica 2 0.0 0.91472 0.0 0.14149 1.0 0.82369   0.59397 151 151 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc bulk bulk   Taiwan 2022-11-22 Adult Adult Heart Cardiovascular System
72125 72125 SRR22366735 SRX18337362 SRS15826347 SRP407292 PRJNA900299 Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration PRJNA900299 Other Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.     single cell RNA seq of macrophage and neutrophil cells sorted from 1 day post injured zebrafish heart with PBS condition single cell RNA seq of macrophage and neutrophil cells sorted from 1 day post injured zebrafish heart with PBS condition sc PBS 1dpci   strain:wild type AB|age:3 month to 1 year old|sex:male and female|tissue:heart|cell type:macrophage and neutrophil|treatment:1day post cryoinjured heart with PBS condition|BioSampleModel:Model organism or animal                 single cell RNA seq of macrophage and neutrophil cells sorted from 1 day post zebrafish injured heart in PBS condition KO 10X GEX ZBNMPBS1dpci KO 10X GEX ZBNMPBS1dpci 1 day post cryoinjured PBS     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP407292     KO_10X_GEX_ZBNMPBS1dpci_S7_L002_I1_001.fastq.gz KO_10X_GEX_ZBNMPBS1dpci_S7_L002_I2_001.fastq.gz KO_10X_GEX_ZBNMPBS1dpci_S7_L002_R1_001.fastq.gz KO_10X_GEX_ZBNMPBS1dpci_S7_L002_R2_001.fastq.gz fastq fastq fastq fastq 124280694174.0 390819793.0 KO 10X GEX ZBNMPBS1dpci S7 L002 I1 001.fastq.gz 0:8 1:8 2:151 3:151 A:50504338257;C:20602333071;G:20112647801;T:26807443112;N:815245 8 8 151 151 50504338257 20602333071 20112647801 26807443112 815245 SRX18337362 SRS15826347 SRA1544923 Academia Sinica|Institute of Biomedical Sciences Academia Sinica 2 0.0 0.9161 0.0 0.14822 1.0 0.81891   0.59781 151 151 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc bulk bulk   Taiwan 2022-11-23 Adult Adult Heart Cardiovascular System
72126 72126 SRR22366736 SRX18337361 SRS15826346 SRP407292 PRJNA900299 Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration PRJNA900299 Other Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.     single cell RNA seq of macrophage and neutrophil cells sorted from untouched zebrafish heart single cell RNA seq of macrophage and neutrophil cells sorted from untouched zebrafish heart sc UT   strain:wild type AB|age:3 month to 1 year old|sex:male and female|tissue:heart|cell type:macrophage and neutrophil|treatment:wild type heart|BioSampleModel:Model organism or animal                 single cell RNA seq of macrophage and neutrophil cells sorted from zebrafish wild type heart KO 10X GEX ZBNM WT KO 10X GEX ZBNM WT wild type     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP407292     KO_10X_GEX_ZBNM_WT_S5_L002_I1_001.fastq.gz KO_10X_GEX_ZBNM_WT_S5_L002_I2_001.fastq.gz KO_10X_GEX_ZBNM_WT_S5_L002_R1_001.fastq.gz KO_10X_GEX_ZBNM_WT_S5_L002_R2_001.fastq.gz fastq fastq fastq fastq 146800238142.0 461635969.0 KO 10X GEX ZBNM WT S5 L002 I1 001.fastq.gz 0:8 1:8 2:151 3:151 A:60009342670;C:24155451853;G:23489314793;T:31758989136;N:964186 8 8 151 151 60009342670 24155451853 23489314793 31758989136 964186 SRX18337361 SRS15826346 SRA1544923 Academia Sinica|Institute of Biomedical Sciences Academia Sinica 2 0.0 0.90338 0.0 0.17611 1.0 0.83189   0.53987 151 151 T B mate1 technical by mapping diff illumina hiseq_era unknown poly_a unknown sc bulk bulk   Taiwan 2022-11-23 Adult Adult Heart Cardiovascular System
72127 72127 SRR22258543 SRX18235012 SRS15731052 SRP407292 PRJNA900299 Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration PRJNA900299 Other Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.     21day post cryoinjuried 21day post cryoinjuried zebrafish heart tissues in CL CL 21dpci 2   strain:wild type AB|age:3 month to 1 year old|sex:male and female|tissue:heart|treatment:CL|replicate:biological replicate 2|time point:21|BioSampleModel:Model organism or animal                 CL 21dpci replicate 2 ST19 PZ08 ST19 PZ08 CL 21day post cryoinjuried     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP407292     LTS19-PZ08_342bp_S6_L001_R1_001.fastq.gz LTS19-PZ08_342bp_S6_L001_R2_001.fastq.gz fastq fastq 5195592665.0 18109093.0 LTS19 PZ08 342bp S6 L001 R1 001.fastq.gz 0:143.46 1:143.44 A:1373923181;C:1222085937;G:1218114278;T:1381061989;N:407280 143 143     1373923181 1222085937 1218114278 1381061989 407280 SRX18235012 SRS15731052 SRA1538914 Academia Sinica|Institute of Biomedical Sciences Academia Sinica 2 0.95246 0.95377 0.06297 0.06239 0.74255 0.7432 0.51136 0.5225 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   Taiwan 2022-11-10 Adult Adult Heart Cardiovascular System
72128 72128 SRR22258544 SRX18235011 SRS15731051 SRP407292 PRJNA900299 Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration PRJNA900299 Other Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.     21day post cryoinjuried 21day post cryoinjuried zebrafish heart tissues in CL CL 21dpci 1   strain:wild type AB|age:3 month to 1 year old|sex:male and female|tissue:heart|treatment:CL|replicate:biological replicate 1|time point:21|BioSampleModel:Model organism or animal                 CL 21dpci replicate 1 ST19 PZ07 ST19 PZ07 CL 21day post cryoinjuried     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP407292     LTS19-PZ07_342bp_S5_L001_R1_001.fastq.gz LTS19-PZ07_342bp_S5_L001_R2_001.fastq.gz fastq fastq 5847932195.0 20521417.0 LTS19 PZ07 342bp S5 L001 R1 001.fastq.gz 0:142.49 1:142.48 A:1557694924;C:1364216352;G:1360378421;T:1565173611;N:468887 142 142     1557694924 1364216352 1360378421 1565173611 468887 SRX18235011 SRS15731051 SRA1538914 Academia Sinica|Institute of Biomedical Sciences Academia Sinica 2 0.95128 0.95406 0.05502 0.05513 0.74961 0.75065 0.53433 0.52784 132 132 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   Taiwan 2022-11-10 Adult Adult Heart Cardiovascular System
72129 72129 SRR22258545 SRX18235010 SRS15731050 SRP407292 PRJNA900299 Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration PRJNA900299 Other Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.     7day post cryoinjuried 7day post cryoinjuried zebrafish heart tissues in CL CL 7dpci 2   strain:wild type AB|age:3 month to 1 year old|sex:male and female|tissue:heart|treatment:CL|replicate:biological replicate 2|time point:7|BioSampleModel:Model organism or animal                 CL 7dpci replicate 2 ST19 PZ04 ST19 PZ04 CL 7day post cryoinjuried     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP407292     LTS19-PZ04_346bp_S3_L001_R1_001.fastq.gz LTS19-PZ04_346bp_S3_L001_R2_001.fastq.gz fastq fastq 5682245028.0 19757381.0 LTS19 PZ04 346bp S3 L001 R1 001.fastq.gz 0:143.81 1:143.79 A:1506211555;C:1333061413;G:1328552313;T:1513979493;N:440254 143 143     1506211555 1333061413 1328552313 1513979493 440254 SRX18235010 SRS15731050 SRA1538914 Academia Sinica|Institute of Biomedical Sciences Academia Sinica 2 0.95272 0.95528 0.06697 0.06705 0.73805 0.73872 0.50736 0.50719 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   Taiwan 2022-11-10 Adult Adult Heart Cardiovascular System
72130 72130 SRR22258546 SRX18235009 SRS15731049 SRP407292 PRJNA900299 Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration PRJNA900299 Other Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.     7day post cryoinjuried 7day post cryoinjuried zebrafish heart tissues in CL CL 7dpci 1   strain:wild type AB|age:3 month to 1 year old|sex:male and female|tissue:heart|treatment:CL|replicate:biological replicate 1|time point:7|BioSampleModel:Model organism or animal                 CL 7dpci replicate 1 ST19 PZ03 ST19 PZ03 CL 7day post cryoinjuried     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP407292     LTS19-PZ03_339bp_S2_L001_R1_001.fastq.gz LTS19-PZ03_339bp_S2_L001_R2_001.fastq.gz fastq fastq 5958830725.0 20832124.0 LTS19 PZ03 339bp S2 L001 R1 001.fastq.gz 0:143.03 1:143.01 A:1576701130;C:1401162502;G:1396209763;T:1584278806;N:478524 143 143     1576701130 1401162502 1396209763 1584278806 478524 SRX18235009 SRS15731049 SRA1538914 Academia Sinica|Institute of Biomedical Sciences Academia Sinica 2 0.95027 0.95219 0.0614 0.06132 0.73645 0.73799 0.51433 0.51365 127 127 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   Taiwan 2022-11-10 Adult Adult Heart Cardiovascular System
72131 72131 SRR22258547 SRX18235008 SRS15731048 SRP407292 PRJNA900299 Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration PRJNA900299 Other Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.     21day post cryoinjuried 21day post cryoinjuried zebrafish heart tissues in PBS PBS 21dpci 3   strain:wild type AB|age:3 month to 1 year old|sex:male and female|tissue:heart|treatment:PBS|replicate:biological replicate 2|time point:21|BioSampleModel:Model organism or animal                 PBS 21dpci replicate 2 ST19 PZ06 ST19 PZ06 PBS 21day post cryoinjuried     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP407292     LTS19-PZ06_350bp_S4_L001_R1_001.fastq.gz LTS19-PZ06_350bp_S4_L001_R2_001.fastq.gz fastq fastq 5924347433.0 20582889.0 LTS19 PZ06 350bp S4 L001 R1 001.fastq.gz 0:143.92 1:143.90 A:1572809162;C:1387645390;G:1383614310;T:1579804471;N:474100 143 143     1572809162 1387645390 1383614310 1579804471 474100 SRX18235008 SRS15731048 SRA1538914 Academia Sinica|Institute of Biomedical Sciences Academia Sinica 2 0.95121 0.95404 0.05501 0.05461 0.75246 0.7528 0.5154 0.50749 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   Taiwan 2022-11-10 Adult Adult Heart Cardiovascular System
72132 72132 SRR22258548 SRX18235007 SRS15731047 SRP407292 PRJNA900299 Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration PRJNA900299 Other Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.     21day post cryoinjuried 21day post cryoinjuried zebrafish heart tissues in PBS PBS 21dpci 1   strain:wild type AB|age:3 month to 1 year old|sex:male and female|tissue:heart|treatment:PBS|replicate:biological replicate 1|time point:21|BioSampleModel:Model organism or animal                 PBS 21dpci replicate 1 ST19 QF02 ST19 QF02 PBS 21day post cryoinjuried     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP407292     LTS19-QF02_340bp_S10_L001_R1_001.fastq.gz LTS19-QF02_340bp_S10_L001_R2_001.fastq.gz fastq fastq 5232519416.0 18312949.0 LTS19 QF02 340bp S10 L001 R1 001.fastq.gz 0:142.87 1:142.86 A:1380634268;C:1233894781;G:1231023543;T:1386544969;N:421855 142 142     1380634268 1233894781 1231023543 1386544969 421855 SRX18235007 SRS15731047 SRA1538914 Academia Sinica|Institute of Biomedical Sciences Academia Sinica 2 0.95743 0.9589 0.05064 0.0507 0.75848 0.75962 0.50117 0.50139 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   Taiwan 2022-11-10 Adult Adult Heart Cardiovascular System
72133 72133 SRR22258549 SRX18235006 SRS15731046 SRP407292 PRJNA900299 Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration PRJNA900299 Other Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.     7day post cryoinjuried 7day post cryoinjuried zebrafish heart tissues in PBS PBS 7dpci 3   strain:wild type AB|age:3 month to 1 year old|sex:male and female|tissue:heart|treatment:PBS|replicate:biological replicate 2|time point:7|BioSampleModel:Model organism or animal                 PBS 7dpci replicate 2 ST19 PZ02 ST19 PZ02 PBS 7day post cryoinjuried     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP407292     LTS19-PZ02_342bp_S1_L001_R1_001.fastq.gz LTS19-PZ02_342bp_S1_L001_R2_001.fastq.gz fastq fastq 4506352400.0 15784899.0 LTS19 PZ02 342bp S1 L001 R1 001.fastq.gz 0:142.75 1:142.73 A:1192740332;C:1059366674;G:1055797909;T:1198088750;N:358735 142 142     1192740332 1059366674 1055797909 1198088750 358735 SRX18235006 SRS15731046 SRA1538914 Academia Sinica|Institute of Biomedical Sciences Academia Sinica 2 0.95404 0.9561 0.06073 0.0604 0.73996 0.74091 0.50416 0.51058 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   Taiwan 2022-11-10 Adult Adult Heart Cardiovascular System
72134 72134 SRR22258550 SRX18235005 SRS15731045 SRP407292 PRJNA900299 Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration PRJNA900299 Other Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.     7day post cryoinjuried 7day post cryoinjuried zebrafish heart tissues in PBS PBS 7dpci 2   strain:wild type AB|age:3 month to 1 year old|sex:male and female|tissue:heart|treatment:PBS|replicate:biological replicate 1|time point:7|BioSampleModel:Model organism or animal                 PBS 7dpci replicate 1 ST19 QF01 ST19 QF01 PBS 7day post cryoinjuried     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP407292     LTS19-QF01_333bp_S9_L001_R1_001.fastq.gz LTS19-QF01_333bp_S9_L001_R2_001.fastq.gz fastq fastq 4033144990.0 14237954.0 LTS19 QF01 333bp S9 L001 R1 001.fastq.gz 0:141.64 1:141.63 A:1049112811;C:966269165;G:964560615;T:1052856084;N:346315 141 141     1049112811 966269165 964560615 1052856084 346315 SRX18235005 SRS15731045 SRA1538914 Academia Sinica|Institute of Biomedical Sciences Academia Sinica 2 0.95546 0.95753 0.04902 0.04892 0.75112 0.75278 0.4969 0.49486 151 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   Taiwan 2022-11-10 Adult Adult Heart Cardiovascular System
72135 72135 SRR22258551 SRX18235004 SRS15731044 SRP407292 PRJNA900299 Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration PRJNA900299 Other Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.     wild type wild type untouched zebrafish heart tissues UT 3   strain:wild type AB|age:3 month to 1 year old|sex:male and female|tissue:heart|treatment:untouched|replicate:biological replicate 2|time point:0|BioSampleModel:Model organism or animal                 untouched replicate 2 LTS19 PZ10 LTS19 PZ10 untouched     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP407292     LTS19-PZ10_348bp_S8_L001_R1_001.fastq.gz LTS19-PZ10_348bp_S8_L001_R2_001.fastq.gz fastq fastq 6431148822.0 22382395.0 LTS19 PZ10 348bp S8 L001 R1 001.fastq.gz 0:143.67 1:143.66 A:1713776212;C:1499888564;G:1494859035;T:1722122217;N:502794 143 143     1713776212 1499888564 1494859035 1722122217 502794 SRX18235004 SRS15731044 SRA1538914 Academia Sinica|Institute of Biomedical Sciences Academia Sinica 2 0.95513 0.95735 0.0516 0.05112 0.76514 0.76621 0.53925 0.5384 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   Taiwan 2022-11-10 Adult Adult Heart Cardiovascular System
72136 72136 SRR22258552 SRX18235003 SRS15731043 SRP407292 PRJNA900299 Comparative single cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration PRJNA900299 Other Zebrafish exhibit a robust ability to regenerate their hearts following injury and the immunesystem plays a key role in this process. We previously showed that delaying macrophage recruitmentby clodronate liposome CL treatment compromises neutrophil resolution and heart regeneration even when the infiltrating macrophage number was restored within the first xxx post injury Lai etal. 2017. Here we examined the molecular mechanisms underlying the cardiac repair of regenerativePBS control hearts vs. non regenerative CL treated hearts. Bulk transcriptomic analyses revealed thatCL treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiacrepair. Temporal single cell profiling of inflammatory cells in regenerative vs. non regenerativeconditions further identified heterogenous macrophages and neutrophils with distinct infiltrationdynamics gene expression and cellular crosstalk. Among them two residential macrophagesubpopulations were enriched in regenerative hearts and barely recovered in non regenerative hearts.Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of residentmacrophages without xxx the circulating macrophage recruitment to the injured area. Strikingly these resident macrophage deficient zebrafish still exhibited compromised neovascularization and scarresolution. Our results characterized the inflammatory cells of the zebrafish injured hearts andidentified key resident macrophage subpopulations prerequisite for successful heart regeneration.     wild type wild type untouched zebrafish heart tissues UT 2   strain:wild type AB|age:3 month to 1 year old|sex:male and female|tissue:heart|treatment:untouched|replicate:biological replicate 1|time point:0|BioSampleModel:Model organism or animal                 untouched replicate 1 LTS19 PZ09 LTS19 PZ09 untouched     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP407292     LTS19-PZ09_348bp_S7_L001_R1_001.fastq.gz LTS19-PZ09_348bp_S7_L001_R2_001.fastq.gz fastq fastq 7338570795.0 25572611.0 LTS19 PZ09 348bp S7 L001 R1 001.fastq.gz 0:143.49 1:143.48 A:1951207826;C:1715917058;G:1710396299;T:1960476117;N:573495 143 143     1951207826 1715917058 1710396299 1960476117 573495 SRX18235003 SRS15731043 SRA1538914 Academia Sinica|Institute of Biomedical Sciences Academia Sinica 2 0.95558 0.95877 0.05288 0.05289 0.75885 0.75958 0.51637 0.51715 151 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   Taiwan 2022-11-10 Adult Adult Heart Cardiovascular System
76356 76356 SRR24844103 SRX20608301 SRS17908187 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       LB023 mutant B LB023 Mut B   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense MutantB|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 missense mutant: male testes LB023 Mut B LB023 Mut B Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     LB023-Mut-B_R1_001.fastq.gz LB023-Mut-B_R2_001.fastq.gz fastq fastq 5532352200.0 18441174.0 LB023 Mut B R1 001.fastq.gz 0:150 1:150 A:1408144772;C:1348146392;G:1440174663;T:1335799503;N:86870 150 150     1408144772 1348146392 1440174663 1335799503 86870 SRX20608301 SRS17908187 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.93072 0.9289 0.0921 0.09129 0.73129 0.73143 0.55139 0.54723 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76357 76357 SRR24844100 SRX20608300 SRS17908192 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       LB023 mutant C LB023 Mut C   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense MutantC|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 missense mutant: male testes LB023 Mut C LB023 Mut C Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     LB023-Mut-C_R2_001.fastq.gz LB023-Mut-C_R1_001.fastq.gz fastq fastq 6159317100.0 20531057.0 LB023 Mut C R1 001.fastq.gz 0:150 1:150 A:1639865405;C:1424690953;G:1522945570;T:1571725037;N:90135 150 150     1639865405 1424690953 1522945570 1571725037 90135 SRX20608300 SRS17908192 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.92565 0.92502 0.07339 0.0724 0.70832 0.70924 0.50224 0.49923 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76358 76358 SRR24844101 SRX20608299 SRS17908193 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       LB023 wildtype sibling control D LB023 WT D   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense WildtypeD|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 missense wildtype sibling: male testes LB023 WT D LB023 WT D Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     LB023-WT-D_R2_001.fastq.gz LB023-WT-D_R1_001.fastq.gz fastq fastq 5436242700.0 18120809.0 LB023 WT D R1 001.fastq.gz 0:150 1:150 A:1448689171;C:1252673824;G:1358298822;T:1376497051;N:83832 150 150     1448689171 1252673824 1358298822 1376497051 83832 SRX20608299 SRS17908193 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.91802 0.91762 0.09407 0.09394 0.70916 0.7108 0.54977 0.55217 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76359 76359 SRR24844102 SRX20608298 SRS17908191 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       adad1 mutant E adad1 Mut E   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:MutantE|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 mutant: male testes adad1 Mut E adad1 Mut E Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     adad1-Mut-E_R2_001.fastq.gz adad1-Mut-E_R1_001.fastq.gz fastq fastq 4958837100.0 16529457.0 adad1 Mut E R1 001.fastq.gz 0:150 1:150 A:1311870356;C:1151609197;G:1254712533;T:1240567756;N:77258 150 150     1311870356 1151609197 1254712533 1240567756 77258 SRX20608298 SRS17908191 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.901 0.90124 0.11096 0.11139 0.71851 0.71967 0.5526 0.57121 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76360 76360 SRR24844104 SRX20608297 SRS17908190 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       adad1 mutant F adad1 Mut F   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:MutantF|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 mutant: male testes adad1 Mut F adad1 Mut F Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     adad1-Mut-F_R1_001.fastq.gz adad1-Mut-F_R2_001.fastq.gz fastq fastq 5780694600.0 19268982.0 adad1 Mut F R1 001.fastq.gz 0:150 1:150 A:1502665613;C:1371103253;G:1490414769;T:1416422204;N:88761 150 150     1502665613 1371103253 1490414769 1416422204 88761 SRX20608297 SRS17908190 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.89657 0.89588 0.10966 0.10896 0.72671 0.72728 0.57267 0.55033 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76361 76361 SRR24844105 SRX20608296 SRS17908189 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       adad1 wildtype sibling control A adad1 WT A   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:WildtypeA|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 wildtype sibling: male testes adad1 WT A adad1 WT A Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     adad1-WT-A_R1_001.fastq.gz adad1-WT-A_R2_001.fastq.gz fastq fastq 8011954200.0 26706514.0 adad1 WT A R1 001.fastq.gz 0:150 1:150 A:2090202005;C:1898897650;G:2026356221;T:1996371474;N:126850 150 150     2090202005 1898897650 2026356221 1996371474 126850 SRX20608296 SRS17908189 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.91189 0.91021 0.06102 0.06139 0.68525 0.68718 0.50676 0.50889 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76362 76362 SRR24844106 SRX20608295 SRS17908186 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       adad1 wildtype sibling control B adad1 WT B   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:WildtypeB|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 wildtype sibling: male testes adad1 WT B adad1 WT B Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     adad1-WT-B_R1_001.fastq.gz adad1-WT-B_R2_001.fastq.gz fastq fastq 7492292100.0 24974307.0 adad1 WT B R1 001.fastq.gz 0:150 1:150 A:1943185783;C:1771813934;G:1904551325;T:1872624369;N:116689 150 150     1943185783 1771813934 1904551325 1872624369 116689 SRX20608295 SRS17908186 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.90916 0.90763 0.11162 0.11123 0.67399 0.6743 0.52068 0.52927 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76363 76363 SRR24844107 SRX20608294 SRS17908185 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       adad1 wildtype sibling control C adad1 WT C   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:WildtypeC|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 wildtype sibling: male testes adad1 WT C adad1 WT C Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     adad1-WT-C_R2_001.fastq.gz adad1-WT-C_R1_001.fastq.gz fastq fastq 7521501900.0 25071673.0 adad1 WT C R1 001.fastq.gz 0:150 1:150 A:1804312038;C:1905161135;G:2076680572;T:1735230886;N:117269 150 150     1804312038 1905161135 2076680572 1735230886 117269 SRX20608294 SRS17908185 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.91415 0.91424 0.1126 0.11157 0.72861 0.72924 0.60581 0.59123 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76364 76364 SRR24844111 SRX20608293 SRS17908188 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       adad1 wildtype sibling control D adad1 WT D   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:WildtypeD|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 wildtype sibling: male testes adad1 WT D adad1 WT D Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     adad1-WT-D_R2_001.fastq.gz adad1-WT-D_R1_001.fastq.gz fastq fastq 6723661500.0 22412205.0 adad1 WT D R1 001.fastq.gz 0:150 1:150 A:1762783841;C:1577461245;G:1700257202;T:1683053935;N:105277 150 150     1762783841 1577461245 1700257202 1683053935 105277 SRX20608293 SRS17908188 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.90669 0.90515 0.1057 0.1054 0.7055 0.70648 0.53378 0.53859 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76365 76365 SRR24844108 SRX20608292 SRS17908183 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       LB023 wildtype sibling control C LB023 WT C   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense WildtypeC|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 missense wildtype sibling: male testes LB023 WT C LB023 WT C Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     LB023-WT-C_R1_001.fastq.gz LB023-WT-C_R2_001.fastq.gz fastq fastq 6931350600.0 23104502.0 LB023 WT C R1 001.fastq.gz 0:150 1:150 A:1738105921;C:1615563430;G:1915220365;T:1662351851;N:109033 150 150     1738105921 1615563430 1915220365 1662351851 109033 SRX20608292 SRS17908183 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.85918 0.86008 0.0973 0.0972 0.75621 0.75617 0.51414 0.52127 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76366 76366 SRR24844109 SRX20608291 SRS17908182 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       LB023 wildtype sibling control B LB023 WT B   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense WildtypeB|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 missense wildtype sibling: male testes LB023 WT B LB023 WT B Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     LB023-WT-B_R1_001.fastq.gz LB023-WT-B_R2_001.fastq.gz fastq fastq 6486567300.0 21621891.0 LB023 WT B R1 001.fastq.gz 0:150 1:150 A:1659315544;C:1565803285;G:1669608945;T:1591739895;N:99631 150 150     1659315544 1565803285 1669608945 1591739895 99631 SRX20608291 SRS17908182 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.92214 0.92196 0.09064 0.09079 0.70092 0.70207 0.54638 0.55145 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76367 76367 SRR24844110 SRX20608290 SRS17908184 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       LB023 wildtype sibling control A LB023 WT A   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense WildtypeA|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 missense wildtype sibling: male testes LB023 WT A LB023 WT A Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     LB023-WT-A_R1_001.fastq.gz LB023-WT-A_R2_001.fastq.gz fastq fastq 7085531700.0 23618439.0 LB023 WT A R1 001.fastq.gz 0:150 1:150 A:1870324648;C:1666204540;G:1769576825;T:1779314498;N:111189 150 150     1870324648 1666204540 1769576825 1779314498 111189 SRX20608290 SRS17908184 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.91831 0.91753 0.06037 0.06044 0.70307 0.70368 0.51531 0.51099 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76368 76368 SRR24844112 SRX20608289 SRS17908179 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       LB023 mutant F LB023 Mut F   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense MutantF|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 missense mutant: male testes LB023 Mut F LB023 Mut F Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     LB023-Mut-F_R1_001.fastq.gz LB023-Mut-F_R2_001.fastq.gz fastq fastq 7753356600.0 25844522.0 LB023 Mut F R1 001.fastq.gz 0:150 1:150 A:2031483621;C:1809017944;G:1970064517;T:1942669709;N:120809 150 150     2031483621 1809017944 1970064517 1942669709 120809 SRX20608289 SRS17908179 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.87475 0.87314 0.09092 0.09089 0.75373 0.75434 0.5602 0.56521 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76369 76369 SRR24844113 SRX20608288 SRS17908178 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       LB023 mutant E LB023 Mut E   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:Missense MutantE|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 missense mutant: male testes LB023 Mut E LB023 Mut E Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     LB023-Mut-E_R1_001.fastq.gz LB023-Mut-E_R2_001.fastq.gz fastq fastq 4532652000.0 15108840.0 LB023 Mut E R1 001.fastq.gz 0:150 1:150 A:1199854650;C:1037858889;G:1150707006;T:1144159494;N:71961 150 150     1199854650 1037858889 1150707006 1144159494 71961 SRX20608288 SRS17908178 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.87501 0.87504 0.08393 0.08384 0.76021 0.76055 0.54045 0.54351 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76370 76370 SRR24844114 SRX20608287 SRS17908181 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       adad1 mutant C adad1 Mut C   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:MutantC|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 mutant: male testes adad1 Mut C adad1 Mut C Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     adad1-Mut-C_R1_001.fastq.gz adad1-Mut-C_R2_001.fastq.gz fastq fastq 7938136500.0 26460455.0 adad1 Mut C R1 001.fastq.gz 0:150 1:150 A:2011717685;C:1935444799;G:2053481206;T:1937375239;N:117571 150 150     2011717685 1935444799 2053481206 1937375239 117571 SRX20608287 SRS17908181 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.92456 0.92396 0.08714 0.08738 0.70575 0.70826 0.5441 0.52561 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System
76371 76371 SRR24844115 SRX20608286 SRS17908180 SRP441411 PRJNA980839 Adad1 knockout and misense mutant RNAseq PRJNA980839 Other The double stranded RNA binding protein Adad1 adenosine deaminase domain containing 1 is a member of the adenosine deaminase acting on RNAs Adar protein family with germ cell specific expression. In mice Adad1 is necessary for sperm differentiation however its function outside of mammals has not been investigated. Here through an N ethyl N nitrosourea ENU based forward genetic screen we identified an adad1 mutant zebrafish line that develop as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish however germ cells populated the gonad proliferated and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes the spermatocytes failed to progress beyond the zygotene stage. Thus Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell LRC assay and found that the mutant testes had fewer LRCs and nanos2 expressing cells compared to wild type siblings suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by maturity. To identify potential molecular processes regulated by Adad1 we sequenced bulk mRNA from mutants and wild type testes and found mis regulation of genes involved in RNA stability and modification pointing to a potential broader role in post transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.       adad1 mutant A adad1 Mut A   strain:Tuebingen|age:45dpf|dev stage:Juvenile|collection date:2021 03|geo loc name:USA:Boston|sex:male|tissue:Testis|genotype:MutantA|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio adad1 mutant: male testes adad1 Mut A adad1 Mut A Total RNA was isolated from 45 dpf adad1Y67X Tg [ziwi:eGFP]uc1 and adad1M392K Tg [ddx4:eGFP] testes using the RNeasy micro kit Qiagen. Since the testes were very small at this age 5 testes were pooled together for each biological replicate 4 biological replicates for each genotype. Isolated RNA was sent to Genewiz at Azenta Life Sciences NJ for library preparation with poly A selection method and 150 bp paired end sequencing on an Illumina HiSeq platform.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP441411     adad1-Mut-A_R1_001.fastq.gz adad1-Mut-A_R2_001.fastq.gz fastq fastq 7254148200.0 24180494.0 adad1 Mut A R1 001.fastq.gz 0:150 1:150 A:1849587944;C:1771248935;G:1861148471;T:1772049096;N:113754 150 150     1849587944 1771248935 1861148471 1772049096 113754 SRX20608286 SRS17908180 SRA1650047 University of Massachusetts Boston|Biology University of Massachusetts Boston 2 0.93069 0.93108 0.10454 0.10422 0.69899 0.70088 0.53698 0.55029 150 150 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2023-06-07 Juvenile Juvenile Gonad Reproductive System

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

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