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,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,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,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,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,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,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,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,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,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,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
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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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