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706 rows where devstage_curation_coarse = "Adult" and tissue_curation = "Kidney"

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technology 8

experiment.library_selection 6

experiment.platform 4

experiment.library_strategy 3

experiment.library_source 3

experiment.library_layout 2

devstage_curation 2

tissue_curation_coarse 1

tissue_curation 1

  • Kidney · 706 ✖

devstage_curation_coarse 1

  • Adult · 706 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
8067 8067 ERR035547 ERX013537 ERS017858 ERP000447 PRJEB2368 Sanger zebrafish sequencing E-MTAB-460 Other       Protocols: Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Zebrafish adult head kidney SAMEA782572 Wellcome Sanger Institute ENA first public:2011 02 03|ENA last update:2018 03 08|External Id:SAMEA782572|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 02 03T12:40:41Z|INSDC last update:2018 03 08T15:25:22Z|INSDC status:public|StrainOrLine:Singapore|Submitter Id:E MTAB 460:Zebrafish adult head kidney|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:head kidney|sample name:E MTAB 460:Zebrafish adult head kidney|sex:mixed                 Sanger zebrafish sequencing E MTAB 460 part2:5625 3 ZFheadkidney 2 RNA 1523494 Sanger zebrafish sequencing Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was enriched for polyA+ RNA by 2 rounds of polyA pull down with magnetic beads and included a DNase treatment between the 2 rounds. RNA was chemically fragmented LiCl precipitated reverse transcribed with random primers a second strand synthesized and made into a standard Illumina library with a fragment size of 250 to 300 bp. Experimental Factor: ORGANISM PART:head kidney RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>2</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>85</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP000447 Illumina Genome Analyzer II paired end sequencing; Sanger zebrafish sequencing ENA FIRST PUBLIC:2011 06 14|ENA LAST UPDATE:2018 11 16 5625_3.srf srf 3610226240.0 22563914.0 E MTAB 460 part2:5625 3.srf 0:76 1:8 2:76 A:924866194;C:782403420;G:781277214;T:934812782;N:6355318 76 8 76   924866194 782403420 781277214 934812782 6355318 ERX013537 ERS017858 ERA033503 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.8952 0.89175 0.09427 0.09347 0.70883 0.71121 0.3613 0.35921 76 76 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   United Kingdom 2011-02-03 Adult Adult Kidney Renal System
8072 8072 ERR023146 ERX009446 ERS017858 ERP000447 PRJEB2368 Sanger zebrafish sequencing E-MTAB-460 Other       Protocols: Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Zebrafish adult head kidney SAMEA782572 Wellcome Sanger Institute ENA first public:2011 02 03|ENA last update:2018 03 08|External Id:SAMEA782572|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 02 03T12:40:41Z|INSDC last update:2018 03 08T15:25:22Z|INSDC status:public|StrainOrLine:Singapore|Submitter Id:E MTAB 460:Zebrafish adult head kidney|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:head kidney|sample name:E MTAB 460:Zebrafish adult head kidney|sex:mixed                 Sanger zebrafish sequencing E MTAB 460:3212 8 RNA from Zebrafish adult head kidney Sanger zebrafish sequencing Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Experimental Factor: ORGANISM PART:head kidney RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP000447 Illumina Genome Analyzer II paired end sequencing; Sanger zebrafish sequencing ENA FIRST PUBLIC:2011 02 03|ENA LAST UPDATE:2018 11 16 3212_8.srf srf 1030624600.0 6780425.0 E MTAB 460:3212 8.srf 0:76 1:76 A:349845451;C:160945226;G:157028856;T:352888853;N:9916214 76 76     349845451 160945226 157028856 352888853 9916214 ERX009446 ERS017858 ERA015648 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.84103 0.82642 0.30085 0.29526 0.76094 0.7652 0.56228 0.45561 76 76 B B biological fallback assumption illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2011-02-03 Adult Adult Kidney Renal System
8075 8075 ERR023149 ERX009443 ERS017858 ERP000447 PRJEB2368 Sanger zebrafish sequencing E-MTAB-460 Other       Protocols: Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Zebrafish adult head kidney SAMEA782572 Wellcome Sanger Institute ENA first public:2011 02 03|ENA last update:2018 03 08|External Id:SAMEA782572|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2011 02 03T12:40:41Z|INSDC last update:2018 03 08T15:25:22Z|INSDC status:public|StrainOrLine:Singapore|Submitter Id:E MTAB 460:Zebrafish adult head kidney|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:head kidney|sample name:E MTAB 460:Zebrafish adult head kidney|sex:mixed                 Sanger zebrafish sequencing E MTAB 460:4191 6 RNA from Zebrafish adult head kidney Sanger zebrafish sequencing Zebrafish tissue was collected from Singapore strain incross fish grown at 28C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were re suspended in 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Experimental Factor: ORGANISM PART:head kidney RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP000447 Illumina Genome Analyzer II paired end sequencing; Sanger zebrafish sequencing ENA FIRST PUBLIC:2011 02 03|ENA LAST UPDATE:2018 11 16 4191_6.srf srf 3888911336.0 25584943.0 E MTAB 460:4191 6.srf 0:76 1:76 A:1359993097;C:582070992;G:582686161;T:1356976166;N:7184920 76 76     1359993097 582070992 582686161 1356976166 7184920 ERX009443 ERS017858 ERA015648 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.83678 0.82953 0.3327 0.33041 0.77045 0.77104 0.54977 0.54422 76 76 B B biological fallback assumption illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2011-02-03 Adult Adult Kidney Renal System
10166 10166 ERR5762357 ERX5471113 ERS6291553 ERP128548 PRJEB44492 scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish E-MTAB-10370 Transcriptome Analysis GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice its role during adult hematopoiesis is incompletely understood. In zebrafish mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs. ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09   Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2. wt2 gata2b SAMEA8606934 Erasmus Medical Center ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09|External Id:SAMEA8606934|INSDC center alias:Erasmus Medical Center|INSDC center name:Erasmus Medical Center|INSDC first public:2022 04 09T00:20:19Z|INSDC last update:2022 04 09T00:20:19Z|INSDC status:public|Submitter Id:E MTAB 10370:wt2 gata2b|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|isolate:not applicable|organism part:kidney|sample name:E MTAB 10370:wt2 gata2b|sampling site:kidney marrow|sex:female|strain:AB                 Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish E MTAB 10370:wt2 gata2b p wt2 gata2b p scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC SINGLE CELL PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP128548 Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09 wt2_gata2b.bam bam 25266437196.0 277653156.0 E MTAB 10370:wt2 gata2b 0:91 A:7555470312;C:5144518052;G:5682746714;T:6882396490;N:1305628 91       7555470312 5144518052 5682746714 6882396490 1305628 ERX5471113 ERS6291553 ERA4089475 Erasmus Medical Center|European Nucleotide Archive Erasmus Medical Center|European Nucleotide Archive 1 0.90876   0.18424   0.84017   0.55508   91   B   usable mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   Netherlands 2022-04-09 Adult Adult Kidney Renal System
10167 10167 ERR5762356 ERX5471112 ERS6291552 ERP128548 PRJEB44492 scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish E-MTAB-10370 Transcriptome Analysis GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice its role during adult hematopoiesis is incompletely understood. In zebrafish mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs. ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09   Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2. wt1 gata2b SAMEA8606933 Erasmus Medical Center ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09|External Id:SAMEA8606933|INSDC center alias:Erasmus Medical Center|INSDC center name:Erasmus Medical Center|INSDC first public:2022 04 09T00:20:19Z|INSDC last update:2022 04 09T00:20:19Z|INSDC status:public|Submitter Id:E MTAB 10370:wt1 gata2b|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|isolate:not applicable|organism part:kidney|sample name:E MTAB 10370:wt1 gata2b|sampling site:kidney marrow|sex:female|strain:AB                 Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish E MTAB 10370:wt1 gata2b p wt1 gata2b p scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2. Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC SINGLE CELL PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP128548 Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09 wt1_gata2b.bam bam 36376708095.0 399744045.0 E MTAB 10370:wt1 gata2b 0:91 A:10397161431;C:8128518427;G:8799445454;T:9049686061;N:1896722 91       10397161431 8128518427 8799445454 9049686061 1896722 ERX5471112 ERS6291552 ERA4089475 Erasmus Medical Center|European Nucleotide Archive Erasmus Medical Center|European Nucleotide Archive 1 0.94708   0.08938   0.85449   0.52917   91   B   usable mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   Netherlands 2022-04-09 Adult Adult Kidney Renal System
10168 10168 ERR5762355 ERX5471111 ERS6291551 ERP128548 PRJEB44492 scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish E-MTAB-10370 Transcriptome Analysis GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice its role during adult hematopoiesis is incompletely understood. In zebrafish mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs. ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09   Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2. hom2 gata2b SAMEA8606932 Erasmus Medical Center ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09|External Id:SAMEA8606932|INSDC center alias:Erasmus Medical Center|INSDC center name:Erasmus Medical Center|INSDC first public:2022 04 09T00:20:19Z|INSDC last update:2022 04 09T00:20:19Z|INSDC status:public|Submitter Id:E MTAB 10370:hom2 gata2b|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:gata2b / |isolate:not applicable|organism part:kidney|sample name:E MTAB 10370:hom2 gata2b|sampling site:kidney marrow|sex:female|strain:AB                 Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish E MTAB 10370:hom2 gata2b p hom2 gata2b p scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2. Experimental Factor: genotype:gata2b / RNA-Seq TRANSCRIPTOMIC SINGLE CELL PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP128548 Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09 hom2_gata2b.bam bam 22416887402.0 246339422.0 E MTAB 10370:hom2 gata2b 0:91 A:6732382430;C:4540586585;G:4933684272;T:6209137814;N:1096301 91       6732382430 4540586585 4933684272 6209137814 1096301 ERX5471111 ERS6291551 ERA4089475 Erasmus Medical Center|European Nucleotide Archive Erasmus Medical Center|European Nucleotide Archive 1 0.91306   0.21566   0.83469   0.53782   91   B   usable mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   Netherlands 2022-04-09 Adult Adult Kidney Renal System
10169 10169 ERR5762354 ERX5471110 ERS6291550 ERP128548 PRJEB44492 scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish E-MTAB-10370 Transcriptome Analysis GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice its role during adult hematopoiesis is incompletely understood. In zebrafish mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs. ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09   Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2. hom1 gata2b SAMEA8606931 Erasmus Medical Center ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09|External Id:SAMEA8606931|INSDC center alias:Erasmus Medical Center|INSDC center name:Erasmus Medical Center|INSDC first public:2022 04 09T00:20:19Z|INSDC last update:2022 04 09T00:20:19Z|INSDC status:public|Submitter Id:E MTAB 10370:hom1 gata2b|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:gata2b / |isolate:not applicable|organism part:kidney|sample name:E MTAB 10370:hom1 gata2b|sampling site:kidney marrow|sex:female|strain:AB                 Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish E MTAB 10370:hom1 gata2b p hom1 gata2b p scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2. Experimental Factor: genotype:gata2b / RNA-Seq TRANSCRIPTOMIC SINGLE CELL PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP128548 Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09 hom1_gata2b.bam bam 18004290759.0 197849349.0 E MTAB 10370:hom1 gata2b 0:91 A:5232521408;C:3876317502;G:4287902596;T:4606191653;N:1357600 91       5232521408 3876317502 4287902596 4606191653 1357600 ERX5471110 ERS6291550 ERA4089475 Erasmus Medical Center|European Nucleotide Archive Erasmus Medical Center|European Nucleotide Archive 1 0.94131   0.08871   0.83465   0.52792   91   B   usable mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   Netherlands 2022-04-09 Adult Adult Kidney Renal System
25143 25143 SRR25649164 SRX21375297 SRS18618389 SRP455253 PRJNA1005695 Metagenomic survey of zebrafish from the laboratory and the pet trade PRJNA1005695 Other This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.         18843X5   strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:kidney|isolation source:lab cohoused|replicate:CHM3|BioSampleModel:Model organism or animal                 RNA seq of adult Danio rerio from laboratory and pet trade sources 18843X5 18843X5 Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample     RNA-Seq METATRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP455253     18843X5_R1.fastq.gz 18843X5_R2.fastq.gz fastq fastq 11487744176.0 38038888.0 18843X5 R1.fastq.gz 0:151 1:151 A:3214900282;C:2532228300;G:2651065167;T:3089370892;N:179535 151 151     3214900282 2532228300 2651065167 3089370892 179535 SRX21375297 SRS18618389 SRA1693347 University of Utah|Quantitative Cell Science University of Utah 2 0.91483 0.91311 0.35213 0.35037 0.68347 0.68826 0.49832 0.49905 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk bulk bulk   United States 2023-08-15 Adult Adult Kidney Renal System
25146 25146 SRR25649167 SRX21375294 SRS18618386 SRP455253 PRJNA1005695 Metagenomic survey of zebrafish from the laboratory and the pet trade PRJNA1005695 Other This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.         18843X2   strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:kidney|isolation source:lab cohoused|replicate:CHM2|BioSampleModel:Model organism or animal                 RNA seq of adult Danio rerio from laboratory and pet trade sources 18843X2 18843X2 Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample     RNA-Seq METATRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP455253     18843X2_R2.fastq.gz 18843X2_R1.fastq.gz fastq fastq 8319888298.0 27549299.0 18843X2 R1.fastq.gz 0:151 1:151 A:2316006657;C:1846379220;G:1965504688;T:2191867233;N:130500 151 151     2316006657 1846379220 1965504688 2191867233 130500 SRX21375294 SRS18618386 SRA1693347 University of Utah|Quantitative Cell Science University of Utah 2 0.90385 0.90304 0.30055 0.3001 0.68345 0.6901 0.49306 0.48285 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk bulk bulk   United States 2023-08-15 Adult Adult Kidney Renal System
25150 25150 SRR25649171 SRX21375290 SRS18618382 SRP455253 PRJNA1005695 Metagenomic survey of zebrafish from the laboratory and the pet trade PRJNA1005695 Other This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.         18689X1   strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:kidney|isolation source:lab cohoused|replicate:CHM1|BioSampleModel:Model organism or animal                 RNA seq of adult Danio rerio from laboratory and pet trade sources 18689X1 18689X1 Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample     RNA-Seq METATRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP455253     18689X1_R1.fastq.gz 18689X1_R2.fastq.gz fastq fastq 7723999112.0 25576156.0 18689X1 R1.fastq.gz 0:151 1:151 A:1938376895;C:1923902263;G:1896332244;T:1965229370;N:158340 151 151     1938376895 1923902263 1896332244 1965229370 158340 SRX21375290 SRS18618382 SRA1693347 University of Utah|Quantitative Cell Science University of Utah 2 0.87233 0.87262 0.28456 0.28071 0.73858 0.7414 0.60785 0.61428 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk bulk bulk   United States 2023-08-15 Adult Adult Kidney Renal System
25153 25153 SRR25649174 SRX21375287 SRS18618379 SRP455253 PRJNA1005695 Metagenomic survey of zebrafish from the laboratory and the pet trade PRJNA1005695 Other This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.         18843X8   strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:kidney|isolation source:lab|replicate:CNTM3|BioSampleModel:Model organism or animal                 RNA seq of adult Danio rerio from laboratory and pet trade sources 18843X8 18843X8 Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample     RNA-Seq METATRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP455253     18843X8_R1.fastq.gz 18843X8_R2.fastq.gz fastq fastq 7615135964.0 25215682.0 18843X8 R1.fastq.gz 0:151 1:151 A:2157897532;C:1663478819;G:1764954395;T:2028683751;N:121467 151 151     2157897532 1663478819 1764954395 2028683751 121467 SRX21375287 SRS18618379 SRA1693347 University of Utah|Quantitative Cell Science University of Utah 2 0.91455 0.91333 0.34885 0.34782 0.69467 0.70167 0.50339 0.51371 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk bulk bulk   United States 2023-08-15 Adult Adult Kidney Renal System
25156 25156 SRR25649177 SRX21375284 SRS18618376 SRP455253 PRJNA1005695 Metagenomic survey of zebrafish from the laboratory and the pet trade PRJNA1005695 Other This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.         18689X3   strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:kidney|isolation source:lab|replicate:CNTM2|BioSampleModel:Model organism or animal                 RNA seq of adult Danio rerio from laboratory and pet trade sources 18689X3 18689X3 Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample     RNA-Seq METATRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP455253     18689X3_R1.fastq.gz 18689X3_R2.fastq.gz fastq fastq 8819353112.0 29203156.0 18689X3 R1.fastq.gz 0:151 1:151 A:2342877591;C:2071139579;G:2035896879;T:2369259787;N:179276 151 151     2342877591 2071139579 2035896879 2369259787 179276 SRX21375284 SRS18618376 SRA1693347 University of Utah|Quantitative Cell Science University of Utah 2 0.85514 0.85429 0.35095 0.34608 0.72985 0.73077 0.51131 0.53375 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk bulk bulk   United States 2023-08-15 Adult Adult Kidney Renal System
25159 25159 SRR25649180 SRX21375281 SRS18618373 SRP455253 PRJNA1005695 Metagenomic survey of zebrafish from the laboratory and the pet trade PRJNA1005695 Other This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.         18689X4   strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:female|tissue:kidney|isolation source:lab|replicate:CNTF1|BioSampleModel:Model organism or animal                 RNA seq of adult Danio rerio from laboratory and pet trade sources 18689X4 18689X4 Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample     RNA-Seq METATRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP455253     18689X4_R1.fastq.gz 18689X4_R2.fastq.gz fastq fastq 9931670150.0 32886325.0 18689X4 R1.fastq.gz 0:151 1:151 A:2494588549;C:2471174839;G:2445771402;T:2519940959;N:194401 151 151     2494588549 2471174839 2445771402 2519940959 194401 SRX21375281 SRS18618373 SRA1693347 University of Utah|Quantitative Cell Science University of Utah 2 0.87391 0.87402 0.31383 0.30879 0.73789 0.74014 0.63365 0.63903 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk bulk bulk   United States 2023-08-15 Adult Adult Kidney Renal System
28589 28589 SRR26491369 SRX22195232 SRS19251247 SRP468071 PRJNA1031138 Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] GSE246039 Transcriptome Analysis Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. parent bioproject:PRJNA814534 pubmed:38280871   KM eos GSM7854254   source name:eosinophils|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing KM eos Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. eosinophils   For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA.   strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP GSM7854254 GSM7854254: KM eos; Danio rerio; RNA Seq GSM7854254 r1 GSM7854254 1 For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP468071   loader:fastq load.py LGF-2-LGF-2-1_L1_1.fq.gz LGF-2-LGF-2-1_L1_2.fq.gz fastq fastq 25680257100.0 85600857.0 GSM7854254 r1 0:150 1:150 A:8025239149;C:3737115767;G:4237725481;T:9679701617;N:475086 150 150     8025239149 3737115767 4237725481 9679701617 475086 SRX22195232 SRS19251247 SRA1739642 South China University of Technology South China University of Technology 2 0.21477 0.87303 0.06136 0.18991 0.99084 0.83187 0.58742 0.60309 150 150 T B mate1 technical by mapping diff illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   China 2023-10-23 Adult Adult Kidney Renal System
28590 28590 SRR26491370 SRX22195232 SRS19251247 SRP468071 PRJNA1031138 Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] GSE246039 Transcriptome Analysis Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. parent bioproject:PRJNA814534 pubmed:38280871   KM eos GSM7854254   source name:eosinophils|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing KM eos Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. eosinophils   For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA.   strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP GSM7854254 GSM7854254: KM eos; Danio rerio; RNA Seq GSM7854254 r1 GSM7854254 1 For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP468071   loader:fastq load.py LGF-2-LGF-2-2_L1_1.fq.gz LGF-2-LGF-2-2_L1_2.fq.gz fastq fastq 30035236200.0 100117454.0 GSM7854254 r2 0:150 1:150 A:9382913917;C:4364910890;G:4955266285;T:11331735278;N:409830 150 150     9382913917 4364910890 4955266285 11331735278 409830 SRX22195232 SRS19251247 SRA1739642 South China University of Technology South China University of Technology 2 0.20279 0.87187 0.05971 0.19015 0.99068 0.83108 0.6129 0.60029 150 150 T B mate1 technical by mapping diff illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   China 2023-10-23 Adult Adult Kidney Renal System
28591 28591 SRR26491371 SRX22195232 SRS19251247 SRP468071 PRJNA1031138 Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] GSE246039 Transcriptome Analysis Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. parent bioproject:PRJNA814534 pubmed:38280871   KM eos GSM7854254   source name:eosinophils|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing KM eos Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. eosinophils   For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA.   strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP GSM7854254 GSM7854254: KM eos; Danio rerio; RNA Seq GSM7854254 r1 GSM7854254 1 For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP468071   loader:fastq load.py LGF-2-LGF-2-3_L1_1.fq.gz LGF-2-LGF-2-3_L1_2.fq.gz fastq fastq 29383046400.0 97943488.0 GSM7854254 r3 0:150 1:150 A:9183968085;C:4275116661;G:4844377300;T:11079048598;N:535756 150 150     9183968085 4275116661 4844377300 11079048598 535756 SRX22195232 SRS19251247 SRA1739642 South China University of Technology South China University of Technology 2 0.19524 0.87384 0.06096 0.19095 0.99188 0.83293 0.58701 0.58361 150 150 T B mate1 technical by mapping diff illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   China 2023-10-23 Adult Adult Kidney Renal System
28592 28592 SRR26491372 SRX22195232 SRS19251247 SRP468071 PRJNA1031138 Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] GSE246039 Transcriptome Analysis Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. parent bioproject:PRJNA814534 pubmed:38280871   KM eos GSM7854254   source name:eosinophils|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing KM eos Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. eosinophils   For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA.   strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP GSM7854254 GSM7854254: KM eos; Danio rerio; RNA Seq GSM7854254 r1 GSM7854254 1 For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP468071   loader:fastq load.py LGF-2-LGF-2-4_L1_1.fq.gz LGF-2-LGF-2-4_L1_2.fq.gz fastq fastq 33167265900.0 110557553.0 GSM7854254 r4 0:150 1:150 A:10380451186;C:4827987987;G:5467300098;T:12490912690;N:613939 150 150     10380451186 4827987987 5467300098 12490912690 613939 SRX22195232 SRS19251247 SRA1739642 South China University of Technology South China University of Technology 2 0.21222 0.87102 0.06704 0.18877 0.99052 0.83343 0.56053 0.58249 150 150 T B mate1 technical by mapping diff illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   China 2023-10-23 Adult Adult Kidney Renal System
28593 28593 SRR26491373 SRX22195231 SRS19251246 SRP468071 PRJNA1031138 Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] GSE246039 Transcriptome Analysis Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. parent bioproject:PRJNA814534 pubmed:38280871   cebpb mut KM 3 GSM7854253   source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1|geo loc name:missing|collection date:missing cebpb mut KM 3 Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. renal cells   For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA.   strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1 GSM7854253 GSM7854253: cebpb mut KM 3; Danio rerio; RNA Seq GSM7854253 r1 GSM7854253 1 For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP468071   loader:fastq load.py b3_S0_L003_R2_001.fastq.gz b3_S0_L003_R1_001.fastq.gz fastq fastq 112688609700.0 375628699.0 GSM7854253 r1 0:150 1:150 A:38960384866;C:23864873253;G:24209853889;T:25652339570;N:1158122 150 150     38960384866 23864873253 24209853889 25652339570 1158122 SRX22195231 SRS19251246 SRA1739642 South China University of Technology South China University of Technology 2 0.0 0.89036 0.0 0.11804 1.0 0.86318   0.69315 150 150 T B mate1 technical by mapping diff illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   China 2023-10-23 Adult Adult Kidney Renal System
28594 28594 SRR26491374 SRX22195230 SRS19251245 SRP468071 PRJNA1031138 Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] GSE246039 Transcriptome Analysis Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. parent bioproject:PRJNA814534 pubmed:38280871   cebpb mut KM 2 GSM7854252   source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1|geo loc name:missing|collection date:missing cebpb mut KM 2 Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. renal cells   For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA.   strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1 GSM7854252 GSM7854252: cebpb mut KM 2; Danio rerio; RNA Seq GSM7854252 r1 GSM7854252 1 For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP468071   loader:fastq load.py b2_S0_L003_R1_001.fastq.gz b2_S0_L003_R2_001.fastq.gz fastq fastq 115982411700.0 386608039.0 GSM7854252 r1 0:150 1:150 A:39966143944;C:23813985234;G:22925287805;T:29275806145;N:1188572 150 150     39966143944 23813985234 22925287805 29275806145 1188572 SRX22195230 SRS19251245 SRA1739642 South China University of Technology South China University of Technology 2 0.0 0.86607 0.0 0.12954 1.0 0.83132   0.631 150 150 T B mate1 technical by mapping diff illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   China 2023-10-23 Adult Adult Kidney Renal System
28595 28595 SRR26491375 SRX22195229 SRS19251244 SRP468071 PRJNA1031138 Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] GSE246039 Transcriptome Analysis Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. parent bioproject:PRJNA814534 pubmed:38280871   cebpb mut KM 1 GSM7854251   source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1|geo loc name:missing|collection date:missing cebpb mut KM 1 Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. renal cells   For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA.   strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1 GSM7854251 GSM7854251: cebpb mut KM 1; Danio rerio; RNA Seq GSM7854251 r1 GSM7854251 1 For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP468071     KMB-KMB-1_FKDL210332848-1a-AK4437_1.fq.gz KMB-KMB-1_FKDL210332848-1a-AK4437_2.fq.gz fastq fastq 17042007300.0 56806691.0 GSM7854251 r1 0:150 1:150 A:5668533017;C:3385304499;G:3366957982;T:4620992880;N:218922 150 150     5668533017 3385304499 3366957982 4620992880 218922 SRX22195229 SRS19251244 SRA1739642 South China University of Technology South China University of Technology 2 0.03184 0.89149 0.00867 0.11757 0.99758 0.82077 0.751 0.57147 150 150 T B mate1 technical by mapping diff illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   China 2023-10-23 Adult Adult Kidney Renal System
28596 28596 SRR26491376 SRX22195229 SRS19251244 SRP468071 PRJNA1031138 Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] GSE246039 Transcriptome Analysis Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. parent bioproject:PRJNA814534 pubmed:38280871   cebpb mut KM 1 GSM7854251   source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1|geo loc name:missing|collection date:missing cebpb mut KM 1 Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. renal cells   For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA.   strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1 GSM7854251 GSM7854251: cebpb mut KM 1; Danio rerio; RNA Seq GSM7854251 r1 GSM7854251 1 For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP468071     KMB-KMB-2_FKDL210332848-1a-AK4438_1.fq.gz KMB-KMB-2_FKDL210332848-1a-AK4438_2.fq.gz fastq fastq 16343762400.0 54479208.0 GSM7854251 r2 0:150 1:150 A:5450512159;C:3242501005;G:3220219102;T:4430319009;N:211125 150 150     5450512159 3242501005 3220219102 4430319009 211125 SRX22195229 SRS19251244 SRA1739642 South China University of Technology South China University of Technology 2 0.02568 0.8936 0.00694 0.11929 0.99776 0.82235 0.66666 0.57382 150 150 T B mate1 technical by mapping diff illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   China 2023-10-23 Adult Adult Kidney Renal System
28597 28597 SRR26491377 SRX22195229 SRS19251244 SRP468071 PRJNA1031138 Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] GSE246039 Transcriptome Analysis Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. parent bioproject:PRJNA814534 pubmed:38280871   cebpb mut KM 1 GSM7854251   source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1|geo loc name:missing|collection date:missing cebpb mut KM 1 Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. renal cells   For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA.   strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1 GSM7854251 GSM7854251: cebpb mut KM 1; Danio rerio; RNA Seq GSM7854251 r1 GSM7854251 1 For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP468071     KMB-KMB-3_FKDL210332848-1a-AK4439_1.fq.gz KMB-KMB-3_FKDL210332848-1a-AK4439_2.fq.gz fastq fastq 10959163500.0 36530545.0 GSM7854251 r3 0:150 1:150 A:3642539220;C:2179136896;G:2168295053;T:2969053386;N:138945 150 150     3642539220 2179136896 2168295053 2969053386 138945 SRX22195229 SRS19251244 SRA1739642 South China University of Technology South China University of Technology 2 0.03232 0.89137 0.00922 0.12039 0.9974 0.82171 0.58775 0.57177 150 150 T B mate1 technical by mapping diff illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   China 2023-10-23 Adult Adult Kidney Renal System
28598 28598 SRR26491378 SRX22195229 SRS19251244 SRP468071 PRJNA1031138 Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] GSE246039 Transcriptome Analysis Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. parent bioproject:PRJNA814534 pubmed:38280871   cebpb mut KM 1 GSM7854251   source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1|geo loc name:missing|collection date:missing cebpb mut KM 1 Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. renal cells   For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA.   strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1 GSM7854251 GSM7854251: cebpb mut KM 1; Danio rerio; RNA Seq GSM7854251 r1 GSM7854251 1 For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP468071     KMB-KMB-4_FKDL210332848-1a-AK4440_1.fq.gz KMB-KMB-4_FKDL210332848-1a-AK4440_2.fq.gz fastq fastq 18130067100.0 60433557.0 GSM7854251 r4 0:150 1:150 A:6030347851;C:3607618024;G:3589047945;T:4902820241;N:233039 150 150     6030347851 3607618024 3589047945 4902820241 233039 SRX22195229 SRS19251244 SRA1739642 South China University of Technology South China University of Technology 2 0.02563 0.89333 0.00745 0.11784 0.99805 0.82156 0.71568 0.56377 150 150 T B mate1 technical by mapping diff illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   China 2023-10-23 Adult Adult Kidney Renal System
28599 28599 SRR26491379 SRX22195228 SRS19251243 SRP468071 PRJNA1031138 Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] GSE246039 Transcriptome Analysis Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. parent bioproject:PRJNA814534 pubmed:38280871   cebp1 mut KM 3 GSM7854250   source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1|geo loc name:missing|collection date:missing cebp1 mut KM 3 Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. renal cells   For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA.   strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1 GSM7854250 GSM7854250: cebp1 mut KM 3; Danio rerio; RNA Seq GSM7854250 r1 GSM7854250 1 For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP468071   loader:fastq load.py e3_S0_L003_R1_001.fastq.gz e3_S0_L003_R2_001.fastq.gz fastq fastq 106692684600.0 355642282.0 GSM7854250 r1 0:150 1:150 A:43760768907;C:19045349028;G:18701042387;T:25183159362;N:2364916 150 150     43760768907 19045349028 18701042387 25183159362 2364916 SRX22195228 SRS19251243 SRA1739642 South China University of Technology South China University of Technology 2 0.0 0.90163 0.0 0.08054 1.0 0.7908   0.55652 150 150 T B mate1 technical by mapping diff illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   China 2023-10-23 Adult Adult Kidney Renal System
28600 28600 SRR26491380 SRX22195227 SRS19251242 SRP468071 PRJNA1031138 Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] GSE246039 Transcriptome Analysis Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. parent bioproject:PRJNA814534 pubmed:38280871   cebp1 mut KM 2 GSM7854249   source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1|geo loc name:missing|collection date:missing cebp1 mut KM 2 Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. renal cells   For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA.   strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1 GSM7854249 GSM7854249: cebp1 mut KM 2; Danio rerio; RNA Seq GSM7854249 r1 GSM7854249 1 For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP468071   loader:fastq load.py e2_S0_L003_R2_001.fastq.gz e2_S0_L003_R1_001.fastq.gz fastq fastq 126515726100.0 421719087.0 GSM7854249 r1 0:150 1:150 A:44391473513;C:24602183317;G:23721160983;T:33799587611;N:1320676 150 150     44391473513 24602183317 23721160983 33799587611 1320676 SRX22195227 SRS19251242 SRA1739642 South China University of Technology South China University of Technology 2 0.0 0.90423 0.0 0.07758 1.0 0.81509   0.5598 150 150 T B mate1 technical by mapping diff illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   China 2023-10-23 Adult Adult Kidney Renal System
28601 28601 SRR26491381 SRX22195226 SRS19251241 SRP468071 PRJNA1031138 Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] GSE246039 Transcriptome Analysis Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. parent bioproject:PRJNA814534 pubmed:38280871   cebp1 mut KM 1 GSM7854248   source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1|geo loc name:missing|collection date:missing cebp1 mut KM 1 Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. renal cells   For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA.   strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1 GSM7854248 GSM7854248: cebp1 mut KM 1; Danio rerio; RNA Seq GSM7854248 r1 GSM7854248 1 For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP468071     KM1-KM1-1_FKDL210332847-1a-AK4772_2.fq.gz KM1-KM1-1_FKDL210332847-1a-AK4772_1.fq.gz fastq fastq 18653393400.0 62177978.0 GSM7854248 r1 0:150 1:150 A:6381285195;C:3802506730;G:3637919666;T:4831413881;N:267928 150 150     6381285195 3802506730 3637919666 4831413881 267928 SRX22195226 SRS19251241 SRA1739642 South China University of Technology South China University of Technology 2 0.0 0.86906 0.0 0.0958 1.0 0.84423   0.5956 150 150 T B mate1 technical by mapping diff illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   China 2023-10-23 Adult Adult Kidney Renal System
28602 28602 SRR26491382 SRX22195226 SRS19251241 SRP468071 PRJNA1031138 Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] GSE246039 Transcriptome Analysis Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. parent bioproject:PRJNA814534 pubmed:38280871   cebp1 mut KM 1 GSM7854248   source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1|geo loc name:missing|collection date:missing cebp1 mut KM 1 Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. renal cells   For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA.   strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1 GSM7854248 GSM7854248: cebp1 mut KM 1; Danio rerio; RNA Seq GSM7854248 r1 GSM7854248 1 For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP468071     KM1-KM1-2_FKDL210332847-1a-AK4773_1.fq.gz KM1-KM1-2_FKDL210332847-1a-AK4773_2.fq.gz fastq fastq 18326971500.0 61089905.0 GSM7854248 r2 0:150 1:150 A:6267364051;C:3758542961;G:3587627310;T:4713172477;N:264701 150 150     6267364051 3758542961 3587627310 4713172477 264701 SRX22195226 SRS19251241 SRA1739642 South China University of Technology South China University of Technology 2 0.0 0.86638 0.0 0.09499 1.0 0.84526   0.60651 150 150 T B mate1 technical by mapping diff illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   China 2023-10-23 Adult Adult Kidney Renal System
28603 28603 SRR26491383 SRX22195226 SRS19251241 SRP468071 PRJNA1031138 Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] GSE246039 Transcriptome Analysis Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. parent bioproject:PRJNA814534 pubmed:38280871   cebp1 mut KM 1 GSM7854248   source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1|geo loc name:missing|collection date:missing cebp1 mut KM 1 Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. renal cells   For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA.   strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1 GSM7854248 GSM7854248: cebp1 mut KM 1; Danio rerio; RNA Seq GSM7854248 r1 GSM7854248 1 For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP468071     KM1-KM1-3_FKDL210332847-1a-AK4774_1.fq.gz KM1-KM1-3_FKDL210332847-1a-AK4774_2.fq.gz fastq fastq 11808660600.0 39362202.0 GSM7854248 r3 0:150 1:150 A:4038900150;C:2417395586;G:2308989220;T:3043205908;N:169736 150 150     4038900150 2417395586 2308989220 3043205908 169736 SRX22195226 SRS19251241 SRA1739642 South China University of Technology South China University of Technology 2 0.0 0.86661 0.0 0.09574 1.0 0.84542   0.57797 150 150 T B mate1 technical by mapping diff illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   China 2023-10-23 Adult Adult Kidney Renal System
28604 28604 SRR26491384 SRX22195226 SRS19251241 SRP468071 PRJNA1031138 Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] GSE246039 Transcriptome Analysis Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. parent bioproject:PRJNA814534 pubmed:38280871   cebp1 mut KM 1 GSM7854248   source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1|geo loc name:missing|collection date:missing cebp1 mut KM 1 Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. renal cells   For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA.   strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1 GSM7854248 GSM7854248: cebp1 mut KM 1; Danio rerio; RNA Seq GSM7854248 r1 GSM7854248 1 For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP468071     KM1-KM1-4_FKDL210332847-1a-AK4775_1.fq.gz KM1-KM1-4_FKDL210332847-1a-AK4775_2.fq.gz fastq fastq 13766583900.0 45888613.0 GSM7854248 r4 0:150 1:150 A:4706562659;C:2817183636;G:2693650162;T:3548993544;N:193899 150 150     4706562659 2817183636 2693650162 3548993544 193899 SRX22195226 SRS19251241 SRA1739642 South China University of Technology South China University of Technology 2 0.0 0.86464 0.0 0.09455 1.0 0.84453   0.59712 150 150 T B mate1 technical by mapping diff illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   China 2023-10-23 Adult Adult Kidney Renal System
28605 28605 SRR26491385 SRX22195225 SRS19251240 SRP468071 PRJNA1031138 Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] GSE246039 Transcriptome Analysis Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. parent bioproject:PRJNA814534 pubmed:38280871   WT KM 3 GSM7854247   source name:renal cells|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1|geo loc name:missing|collection date:missing WT KM 3 Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. renal cells   For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA.   strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1 GSM7854247 GSM7854247: WT KM 3; Danio rerio; RNA Seq GSM7854247 r1 GSM7854247 1 For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP468071   loader:fastq load.py w3_S0_L003_R1_001.fastq.gz w3_S0_L003_R2_001.fastq.gz fastq fastq 142550442300.0 475168141.0 GSM7854247 r1 0:150 1:150 A:56961713939;C:27160797921;G:25876430130;T:32548386896;N:3113414 150 150     56961713939 27160797921 25876430130 32548386896 3113414 SRX22195225 SRS19251240 SRA1739642 South China University of Technology South China University of Technology 2 0.0 0.84672 0.0 0.09057 1.0 0.84893   0.64916 150 150 T B mate1 technical by mapping diff illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   China 2023-10-23 Adult Adult Kidney Renal System
28606 28606 SRR26491386 SRX22195224 SRS19251239 SRP468071 PRJNA1031138 Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] GSE246039 Transcriptome Analysis Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. parent bioproject:PRJNA814534 pubmed:38280871   WT KM 2 GSM7854246   source name:renal cells|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1|geo loc name:missing|collection date:missing WT KM 2 Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. renal cells   For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA.   strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1 GSM7854246 GSM7854246: WT KM 2; Danio rerio; RNA Seq GSM7854246 r1 GSM7854246 1 For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP468071   loader:fastq load.py w2_S0_L003_R2_001.fastq.gz w2_S0_L003_R1_001.fastq.gz fastq fastq 110520161400.0 368400538.0 GSM7854246 r1 0:150 1:150 A:44333853620;C:20994101993;G:19951597607;T:25238178463;N:2429717 150 150     44333853620 20994101993 19951597607 25238178463 2429717 SRX22195224 SRS19251239 SRA1739642 South China University of Technology South China University of Technology 2 0.0 0.84344 0.0 0.0961 1.0 0.83485   0.63275 150 150 T B mate1 technical by mapping diff illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   China 2023-10-23 Adult Adult Kidney Renal System
28607 28607 SRR26491387 SRX22195223 SRS19251238 SRP468071 PRJNA1031138 Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] GSE246039 Transcriptome Analysis Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. parent bioproject:PRJNA814534 pubmed:38280871   WT KM 1 GSM7854245   source name:renal cells|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1|geo loc name:missing|collection date:missing WT KM 1 Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. renal cells   For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA.   strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1 GSM7854245 GSM7854245: WT KM 1; Danio rerio; RNA Seq GSM7854245 r1 GSM7854245 1 For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP468071     WKM-WKM-1_BKDL190841222-1a-AK650_1.fq.gz WKM-WKM-1_BKDL190841222-1a-AK650_2.fq.gz fastq fastq 20481536700.0 68271789.0 GSM7854245 r1 0:150 1:150 A:4681473958;C:3918612929;G:6623380714;T:5257792172;N:276927 150 150     4681473958 3918612929 6623380714 5257792172 276927 SRX22195223 SRS19251238 SRA1739642 South China University of Technology South China University of Technology 2 0.0 0.91381 0.0 0.08281 1.0 0.82386   0.55976 150 150 T B mate1 technical by mapping diff illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   China 2023-10-23 Adult Adult Kidney Renal System
28608 28608 SRR26491388 SRX22195223 SRS19251238 SRP468071 PRJNA1031138 Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] GSE246039 Transcriptome Analysis Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. parent bioproject:PRJNA814534 pubmed:38280871   WT KM 1 GSM7854245   source name:renal cells|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1|geo loc name:missing|collection date:missing WT KM 1 Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. renal cells   For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA.   strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1 GSM7854245 GSM7854245: WT KM 1; Danio rerio; RNA Seq GSM7854245 r1 GSM7854245 1 For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP468071     WKM-WKM-2_BKDL190841222-1a-AK651_2.fq.gz WKM-WKM-2_BKDL190841222-1a-AK651_1.fq.gz fastq fastq 24824596500.0 82748655.0 GSM7854245 r2 0:150 1:150 A:5675288010;C:4753602834;G:8033499593;T:6361861422;N:344641 150 150     5675288010 4753602834 8033499593 6361861422 344641 SRX22195223 SRS19251238 SRA1739642 South China University of Technology South China University of Technology 2 0.0 0.9121 0.0 0.08282 1.0 0.82613   0.56378 150 150 T B mate1 technical by mapping diff illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   China 2023-10-23 Adult Adult Kidney Renal System
28609 28609 SRR26491389 SRX22195223 SRS19251238 SRP468071 PRJNA1031138 Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] GSE246039 Transcriptome Analysis Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. parent bioproject:PRJNA814534 pubmed:38280871   WT KM 1 GSM7854245   source name:renal cells|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1|geo loc name:missing|collection date:missing WT KM 1 Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. renal cells   For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA.   strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1 GSM7854245 GSM7854245: WT KM 1; Danio rerio; RNA Seq GSM7854245 r1 GSM7854245 1 For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP468071     WKM-WKM-3_BKDL190841222-1a-AK652_1.fq.gz WKM-WKM-3_BKDL190841222-1a-AK652_2.fq.gz fastq fastq 20574633600.0 68582112.0 GSM7854245 r3 0:150 1:150 A:4698580031;C:3942306152;G:6657096764;T:5276366726;N:283927 150 150     4698580031 3942306152 6657096764 5276366726 283927 SRX22195223 SRS19251238 SRA1739642 South China University of Technology South China University of Technology 2 0.0 0.9136 0.0 0.08366 1.0 0.82373   0.55683 150 150 T B mate1 technical by mapping diff illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   China 2023-10-23 Adult Adult Kidney Renal System
28610 28610 SRR26491390 SRX22195223 SRS19251238 SRP468071 PRJNA1031138 Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] GSE246039 Transcriptome Analysis Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. parent bioproject:PRJNA814534 pubmed:38280871   WT KM 1 GSM7854245   source name:renal cells|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1|geo loc name:missing|collection date:missing WT KM 1 Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. renal cells   For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA.   strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1 GSM7854245 GSM7854245: WT KM 1; Danio rerio; RNA Seq GSM7854245 r1 GSM7854245 1 For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP468071     WKM-WKM-4_BKDL190841222-1a-AK653_2.fq.gz WKM-WKM-4_BKDL190841222-1a-AK653_1.fq.gz fastq fastq 25381641600.0 84605472.0 GSM7854245 r4 0:150 1:150 A:5785664179;C:4874470993;G:8220023956;T:6501127037;N:355435 150 150     5785664179 4874470993 8220023956 6501127037 355435 SRX22195223 SRS19251238 SRA1739642 South China University of Technology South China University of Technology 2 0.0 0.91371 0.0 0.08381 1.0 0.8244   0.57179 150 150 T B mate1 technical by mapping diff illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   China 2023-10-23 Adult Adult Kidney Renal System
32162 32162 SRR29095835 SRX24619914 SRS21357066 SRP508906 PRJNA1113956 A zebrafish model of diabetic nephropathy PRJNA1113956 Other We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.       6 month zebrafish kidney 1 DN zebrafish   strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal                 6 month zebrafish with proteinuria kidney 4 OF 4 OF 4 6 month zebrafish with proteinuria kidney 4     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   SRP508906     OF_4_1.fq OF_4_2.fq fastq fastq 4377669000.0 14592230.0 OF 4 1.fq 0:150 1:150 A:1194166573;C:999239529;G:1001594280;T:1182651631;N:16987 150 150     1194166573 999239529 1001594280 1182651631 16987 SRX24619914 SRS21357066 SRA1872692 Mie Univeristy|School of Medicine Mie Univeristy                       B B biological fallback assumption illumina novaseq_era unknown unknown unknown bulk unknown unknown   Japan 2024-05-21 Adult Adult Kidney Renal System
32163 32163 SRR29095836 SRX24619913 SRS21357066 SRP508906 PRJNA1113956 A zebrafish model of diabetic nephropathy PRJNA1113956 Other We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.       6 month zebrafish kidney 1 DN zebrafish   strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal                 6 month zebrafish with proteinuria kidney 3 OF 3 OF 3 6 month zebrafish with proteinuria kidney 3     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   SRP508906     OF_3_1.fq OF_3_2.fq fastq fastq 4798165200.0 15993884.0 OF 3 1.fq 0:150 1:150 A:1290466714;C:1114007506;G:1115137813;T:1278535708;N:17459 150 150     1290466714 1114007506 1115137813 1278535708 17459 SRX24619913 SRS21357066 SRA1872692 Mie Univeristy|School of Medicine Mie Univeristy                       B B biological fallback assumption illumina novaseq_era unknown unknown unknown bulk unknown unknown   Japan 2024-05-21 Adult Adult Kidney Renal System
32164 32164 SRR29095837 SRX24619912 SRS21357066 SRP508906 PRJNA1113956 A zebrafish model of diabetic nephropathy PRJNA1113956 Other We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.       6 month zebrafish kidney 1 DN zebrafish   strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal                 6 month zebrafish with proteinuria kidney 2 OF 2 OF 2 6 month zebrafish with proteinuria kidney 2     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   SRP508906     OF_2_1.fq OF_2_2.fq fastq fastq 5661202800.0 18870676.0 OF 2 1.fq 0:150 1:150 A:1549085619;C:1287400217;G:1288853902;T:1535841249;N:21813 150 150     1549085619 1287400217 1288853902 1535841249 21813 SRX24619912 SRS21357066 SRA1872692 Mie Univeristy|School of Medicine Mie Univeristy                       B B biological fallback assumption illumina novaseq_era unknown unknown unknown bulk unknown unknown   Japan 2024-05-21 Adult Adult Kidney Renal System
32165 32165 SRR29095838 SRX24619911 SRS21357066 SRP508906 PRJNA1113956 A zebrafish model of diabetic nephropathy PRJNA1113956 Other We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.       6 month zebrafish kidney 1 DN zebrafish   strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal                 6 month zebrafish with proteinuria kidney 1 OF 1 OF 1 6 month zebrafish with proteinuria kidney 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   SRP508906     OF_1_1.fq OF_1_2.fq fastq fastq 5957895600.0 19859652.0 OF 1 1.fq 0:150 1:150 A:1627320757;C:1359602784;G:1360982917;T:1609967331;N:21811 150 150     1627320757 1359602784 1360982917 1609967331 21811 SRX24619911 SRS21357066 SRA1872692 Mie Univeristy|School of Medicine Mie Univeristy                       B B biological fallback assumption illumina novaseq_era unknown unknown unknown bulk unknown unknown   Japan 2024-05-21 Adult Adult Kidney Renal System
32166 32166 SRR29095839 SRX24619910 SRS21357066 SRP508906 PRJNA1113956 A zebrafish model of diabetic nephropathy PRJNA1113956 Other We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.       6 month zebrafish kidney 1 DN zebrafish   strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal                 6 month zebrafish kidney 4 NF 6 NF 6 6 month zebrafish kidney 4     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   SRP508906     NF_6_1.fq NF_6_2.fq fastq fastq 5469504900.0 18231683.0 NF 6 1.fq 0:150 1:150 A:1480833386;C:1260945093;G:1261275041;T:1466430429;N:20951 150 150     1480833386 1260945093 1261275041 1466430429 20951 SRX24619910 SRS21357066 SRA1872692 Mie Univeristy|School of Medicine Mie Univeristy                       B B biological fallback assumption illumina novaseq_era unknown unknown unknown bulk unknown unknown   Japan 2024-05-21 Adult Adult Kidney Renal System
32167 32167 SRR29095840 SRX24619909 SRS21357066 SRP508906 PRJNA1113956 A zebrafish model of diabetic nephropathy PRJNA1113956 Other We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.       6 month zebrafish kidney 1 DN zebrafish   strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal                 6 month zebrafish kidney 3 NF 5 NF 5 6 month zebrafish kidney 3     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   SRP508906     NF_5_1.fq NF_5_2.fq fastq fastq 6386781900.0 21289273.0 NF 5 1.fq 0:150 1:150 A:1743273279;C:1458330156;G:1460747658;T:1724406616;N:24191 150 150     1743273279 1458330156 1460747658 1724406616 24191 SRX24619909 SRS21357066 SRA1872692 Mie Univeristy|School of Medicine Mie Univeristy                       B B biological fallback assumption illumina novaseq_era unknown unknown unknown bulk unknown unknown   Japan 2024-05-21 Adult Adult Kidney Renal System
32168 32168 SRR29095841 SRX24619908 SRS21357066 SRP508906 PRJNA1113956 A zebrafish model of diabetic nephropathy PRJNA1113956 Other We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.       6 month zebrafish kidney 1 DN zebrafish   strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal                 6 month zebrafish kidney 2 NF 2 NF 2 6 month zebrafish kidney 2     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   SRP508906     NF_2_1.fq NF_2_2.fq fastq fastq 5747851800.0 19159506.0 NF 2 1.fq 0:150 1:150 A:1564796254;C:1316015979;G:1317516650;T:1549501774;N:21143 150 150     1564796254 1316015979 1317516650 1549501774 21143 SRX24619908 SRS21357066 SRA1872692 Mie Univeristy|School of Medicine Mie Univeristy                       B B biological fallback assumption illumina novaseq_era unknown unknown unknown bulk unknown unknown   Japan 2024-05-21 Adult Adult Kidney Renal System
32169 32169 SRR29095842 SRX24619907 SRS21357066 SRP508906 PRJNA1113956 A zebrafish model of diabetic nephropathy PRJNA1113956 Other We created a diabetic nephropathy DN model in zebrafish by crossing diabetic Tgacta1:dnIGF1R EGFP and proteinuria tracing Tgl fabp::VDBP GFPlines named zMIR/VDBP. Overfed adult zMIR/VDBP fish developed severe hyperglycemia and proteinuria which were not observed in wild type zebrafish. Renal histopathology revealed human DN like characteristics such as glomerular basement membrane thickening foot process effacement and glomerular sclerosis. RNA sequencing analysis demonstrated that DN zebrafish kidneys exhibited transcriptional patterns similar to those seen in human DN pathogenesis. Notably the phosphatidylinositol 3 kinase PI3K/protein kinase B Akt signaling pathway was activated a phenomenon observed in the early phase of human DN.       6 month zebrafish kidney 1 DN zebrafish   strain:zMIR/VDBP|age:6 mpf|dev stage:Adult|collection date:2023 03 30|geo loc name:Japan|sex:not determined|tissue:kidney|BioSampleModel:Model organism or animal                 6 month zebrafish kidney 1 NF 1 NF 1 6 month zebrafish kidney 1     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   SRP508906     NF_1_1.fq NF_1_2.fq fastq fastq 5369089800.0 17896966.0 NF 1 1.fq 0:150 1:150 A:1413369042;C:1273865602;G:1277141372;T:1404694133;N:19651 150 150     1413369042 1273865602 1277141372 1404694133 19651 SRX24619907 SRS21357066 SRA1872692 Mie Univeristy|School of Medicine Mie Univeristy                       B B biological fallback assumption illumina novaseq_era unknown unknown unknown bulk unknown unknown   Japan 2024-05-21 Adult Adult Kidney Renal System
32785 32785 SRR29441653 SRX24954080 SRS21657738 SRP514436 PRJNA1125004 A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy GSE270105 Transcriptome Analysis Effective vaccines are urgently needed for the control of tuberculosis TB. Here we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB. Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity but not the canonical DNA damage responses that promote cell death demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably the mRNA vaccine induced autophagy in granulomas coinciding with bacterial killing and cell survival. Collectively these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control PBS control and untreatment control infection 14 days as well as healthy control. Adult zebrafish AB strain 3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5µg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before tr…   pubmed:39759874   M.m infection sample3 GSM8334559   source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:14 days of M.m infection group|treatment:without xxx|geo loc name:missing|collection date:missing M.m infection sample3 The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample kidneys For determination of the host immune response induced by mRNA vaccine therapeutic adult zebrafish AB strain 3 to 4 mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5μg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer’s instructions. The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co. Ltd. Qingdao China and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature ∼28°C pH ∼7.4 and conductivity ∼1500μS. tissue:kidneys|cell type:whole cell immune cell|group:14 days of M.m infection group|treatment:without xxx GSM8334559 GSM8334559: M.m infection sample3; Danio rerio; RNA Seq GSM8334559 r1 GSM8334559 1 post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP514436     M_m_infection_3.R2.fq.gz M_m_infection_3.R1.fq.gz fastq fastq 6356874134.0 21531449.0 GSM8334559 r1 0:147.62 1:147.62 A:1629631082;C:1541934257;G:1557877748;T:1627277838;N:153209 147 147     1629631082 1541934257 1557877748 1627277838 153209 SRX24954080 SRS21657738 SRA1905347 Zhang Lab, Department of Microbiology, Fudan University Zhang Lab, Department of Microbiology, Fudan University 2 0.95052 0.95088 0.05066 0.0508 0.69716 0.6969 0.51335 0.50048 143 143 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-06-17 Adult Adult Kidney Renal System
32786 32786 SRR29441654 SRX24954079 SRS21657737 SRP514436 PRJNA1125004 A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy GSE270105 Transcriptome Analysis Effective vaccines are urgently needed for the control of tuberculosis TB. Here we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB. Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity but not the canonical DNA damage responses that promote cell death demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably the mRNA vaccine induced autophagy in granulomas coinciding with bacterial killing and cell survival. Collectively these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control PBS control and untreatment control infection 14 days as well as healthy control. Adult zebrafish AB strain 3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5µg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before tr…   pubmed:39759874   M.m infection sample2 GSM8334558   source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:14 days of M.m infection group|treatment:without xxx|geo loc name:missing|collection date:missing M.m infection sample2 The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample kidneys For determination of the host immune response induced by mRNA vaccine therapeutic adult zebrafish AB strain 3 to 4 mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5μg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer’s instructions. The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co. Ltd. Qingdao China and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature ∼28°C pH ∼7.4 and conductivity ∼1500μS. tissue:kidneys|cell type:whole cell immune cell|group:14 days of M.m infection group|treatment:without xxx GSM8334558 GSM8334558: M.m infection sample2; Danio rerio; RNA Seq GSM8334558 r1 GSM8334558 1 post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP514436     M_m_infection_2.R2.fq.gz M_m_infection_2.R1.fq.gz fastq fastq 7054524333.0 23848504.0 GSM8334558 r1 0:147.90 1:147.91 A:1815742764;C:1704164760;G:1721079421;T:1813355137;N:182251 147 147     1815742764 1704164760 1721079421 1813355137 182251 SRX24954079 SRS21657737 SRA1905347 Zhang Lab, Department of Microbiology, Fudan University Zhang Lab, Department of Microbiology, Fudan University 2 0.94873 0.9497 0.05329 0.05319 0.70021 0.69897 0.51348 0.51487 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-06-17 Adult Adult Kidney Renal System
32787 32787 SRR29441655 SRX24954078 SRS21657736 SRP514436 PRJNA1125004 A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy GSE270105 Transcriptome Analysis Effective vaccines are urgently needed for the control of tuberculosis TB. Here we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB. Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity but not the canonical DNA damage responses that promote cell death demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably the mRNA vaccine induced autophagy in granulomas coinciding with bacterial killing and cell survival. Collectively these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control PBS control and untreatment control infection 14 days as well as healthy control. Adult zebrafish AB strain 3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5µg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before tr…   pubmed:39759874   M.m infection sample1 GSM8334557   source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:14 days of M.m infection group|treatment:without xxx|geo loc name:missing|collection date:missing M.m infection sample1 The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample kidneys For determination of the host immune response induced by mRNA vaccine therapeutic adult zebrafish AB strain 3 to 4 mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5μg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer’s instructions. The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co. Ltd. Qingdao China and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature ∼28°C pH ∼7.4 and conductivity ∼1500μS. tissue:kidneys|cell type:whole cell immune cell|group:14 days of M.m infection group|treatment:without xxx GSM8334557 GSM8334557: M.m infection sample1; Danio rerio; RNA Seq GSM8334557 r1 GSM8334557 1 post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP514436     M_m_infection_1.R2.fq.gz M_m_infection_1.R1.fq.gz fastq fastq 6946198558.0 23547133.0 GSM8334557 r1 0:147.49 1:147.50 A:1790987034;C:1672981012;G:1691024254;T:1791031433;N:174825 147 147     1790987034 1672981012 1691024254 1791031433 174825 SRX24954078 SRS21657736 SRA1905347 Zhang Lab, Department of Microbiology, Fudan University Zhang Lab, Department of Microbiology, Fudan University 2 0.94915 0.94881 0.05429 0.05404 0.69682 0.69678 0.50968 0.51363 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-06-17 Adult Adult Kidney Renal System
32788 32788 SRR29441656 SRX24954077 SRS21657735 SRP514436 PRJNA1125004 A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy GSE270105 Transcriptome Analysis Effective vaccines are urgently needed for the control of tuberculosis TB. Here we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB. Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity but not the canonical DNA damage responses that promote cell death demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably the mRNA vaccine induced autophagy in granulomas coinciding with bacterial killing and cell survival. Collectively these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control PBS control and untreatment control infection 14 days as well as healthy control. Adult zebrafish AB strain 3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5µg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before tr…   pubmed:39759874   Blank sample3 GSM8334556   source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:Healthy group|treatment:without xxx|geo loc name:missing|collection date:missing Blank sample3 The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample kidneys For determination of the host immune response induced by mRNA vaccine therapeutic adult zebrafish AB strain 3 to 4 mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5μg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer’s instructions. The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co. Ltd. Qingdao China and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature ∼28°C pH ∼7.4 and conductivity ∼1500μS. tissue:kidneys|cell type:whole cell immune cell|group:Healthy group|treatment:without xxx GSM8334556 GSM8334556: Blank sample3; Danio rerio; RNA Seq GSM8334556 r1 GSM8334556 1 post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP514436     Blank3.R2.fq.gz Blank3.R1.fq.gz fastq fastq 6932407082.0 23420695.0 GSM8334556 r1 0:147.99 1:148.00 A:1790632840;C:1666849105;G:1684978083;T:1789775995;N:171059 147 148     1790632840 1666849105 1684978083 1789775995 171059 SRX24954077 SRS21657735 SRA1905347 Zhang Lab, Department of Microbiology, Fudan University Zhang Lab, Department of Microbiology, Fudan University 2 0.94957 0.94988 0.05378 0.05336 0.70715 0.70705 0.52195 0.51293 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-06-17 Adult Adult Kidney Renal System
32789 32789 SRR29441657 SRX24954076 SRS21657734 SRP514436 PRJNA1125004 A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy GSE270105 Transcriptome Analysis Effective vaccines are urgently needed for the control of tuberculosis TB. Here we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB. Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity but not the canonical DNA damage responses that promote cell death demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably the mRNA vaccine induced autophagy in granulomas coinciding with bacterial killing and cell survival. Collectively these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control PBS control and untreatment control infection 14 days as well as healthy control. Adult zebrafish AB strain 3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5µg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before tr…   pubmed:39759874   Blank sample2 GSM8334555   source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:Healthy group|treatment:without xxx|geo loc name:missing|collection date:missing Blank sample2 The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample kidneys For determination of the host immune response induced by mRNA vaccine therapeutic adult zebrafish AB strain 3 to 4 mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5μg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer’s instructions. The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co. Ltd. Qingdao China and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature ∼28°C pH ∼7.4 and conductivity ∼1500μS. tissue:kidneys|cell type:whole cell immune cell|group:Healthy group|treatment:without xxx GSM8334555 GSM8334555: Blank sample2; Danio rerio; RNA Seq GSM8334555 r1 GSM8334555 1 post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP514436     Blank2.R2.fq.gz Blank2.R1.fq.gz fastq fastq 6589805773.0 22282641.0 GSM8334555 r1 0:147.86 1:147.87 A:1700645441;C:1585546539;G:1603218609;T:1700235278;N:159906 147 147     1700645441 1585546539 1603218609 1700235278 159906 SRX24954076 SRS21657734 SRA1905347 Zhang Lab, Department of Microbiology, Fudan University Zhang Lab, Department of Microbiology, Fudan University 2 0.94982 0.94956 0.05437 0.05385 0.69986 0.70003 0.51649 0.51715 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-06-17 Adult Adult Kidney Renal System
32790 32790 SRR29441658 SRX24954075 SRS21657732 SRP514436 PRJNA1125004 A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy GSE270105 Transcriptome Analysis Effective vaccines are urgently needed for the control of tuberculosis TB. Here we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB. Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity but not the canonical DNA damage responses that promote cell death demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably the mRNA vaccine induced autophagy in granulomas coinciding with bacterial killing and cell survival. Collectively these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control PBS control and untreatment control infection 14 days as well as healthy control. Adult zebrafish AB strain 3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5µg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before tr…   pubmed:39759874   Blank sample1 GSM8334554   source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:Healthy group|treatment:without xxx|geo loc name:missing|collection date:missing Blank sample1 The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample kidneys For determination of the host immune response induced by mRNA vaccine therapeutic adult zebrafish AB strain 3 to 4 mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5μg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer’s instructions. The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co. Ltd. Qingdao China and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature ∼28°C pH ∼7.4 and conductivity ∼1500μS. tissue:kidneys|cell type:whole cell immune cell|group:Healthy group|treatment:without xxx GSM8334554 GSM8334554: Blank sample1; Danio rerio; RNA Seq GSM8334554 r1 GSM8334554 1 post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP514436     Blank1.R2.fq.gz Blank1.R1.fq.gz fastq fastq 6988209016.0 23723555.0 GSM8334554 r1 0:147.28 1:147.29 A:1793934528;C:1692773043;G:1711063141;T:1790264470;N:173834 147 147     1793934528 1692773043 1711063141 1790264470 173834 SRX24954075 SRS21657732 SRA1905347 Zhang Lab, Department of Microbiology, Fudan University Zhang Lab, Department of Microbiology, Fudan University 2 0.95053 0.9509 0.04981 0.04955 0.7008 0.7008 0.51262 0.51791 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-06-17 Adult Adult Kidney Renal System
32791 32791 SRR29441659 SRX24954074 SRS21657733 SRP514436 PRJNA1125004 A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy GSE270105 Transcriptome Analysis Effective vaccines are urgently needed for the control of tuberculosis TB. Here we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB. Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity but not the canonical DNA damage responses that promote cell death demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably the mRNA vaccine induced autophagy in granulomas coinciding with bacterial killing and cell survival. Collectively these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control PBS control and untreatment control infection 14 days as well as healthy control. Adult zebrafish AB strain 3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5µg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before tr…   pubmed:39759874   PBS treated sample3 GSM8334553   source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:PBS treated group|treatment:2 dose of PBS immunized|geo loc name:missing|collection date:missing PBS treated sample3 The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample kidneys For determination of the host immune response induced by mRNA vaccine therapeutic adult zebrafish AB strain 3 to 4 mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5μg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer’s instructions. The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co. Ltd. Qingdao China and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature ∼28°C pH ∼7.4 and conductivity ∼1500μS. tissue:kidneys|cell type:whole cell immune cell|group:PBS treated group|treatment:2 dose of PBS immunized GSM8334553 GSM8334553: PBS treated sample3; Danio rerio; RNA Seq GSM8334553 r1 GSM8334553 1 post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP514436     PBS3.R1.fq.gz PBS3.R2.fq.gz fastq fastq 6902483407.0 23381761.0 GSM8334553 r1 0:147.60 1:147.61 A:1789006509;C:1653537037;G:1669979967;T:1789782638;N:177256 147 147     1789006509 1653537037 1669979967 1789782638 177256 SRX24954074 SRS21657733 SRA1905347 Zhang Lab, Department of Microbiology, Fudan University Zhang Lab, Department of Microbiology, Fudan University 2 0.94782 0.94837 0.05863 0.05874 0.70025 0.69899 0.51852 0.51943 91 91 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-06-17 Adult Adult Kidney Renal System
32792 32792 SRR29441660 SRX24954073 SRS21657731 SRP514436 PRJNA1125004 A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy GSE270105 Transcriptome Analysis Effective vaccines are urgently needed for the control of tuberculosis TB. Here we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB. Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity but not the canonical DNA damage responses that promote cell death demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably the mRNA vaccine induced autophagy in granulomas coinciding with bacterial killing and cell survival. Collectively these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control PBS control and untreatment control infection 14 days as well as healthy control. Adult zebrafish AB strain 3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5µg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before tr…   pubmed:39759874   PBS treated sample2 GSM8334552   source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:PBS treated group|treatment:2 dose of PBS immunized|geo loc name:missing|collection date:missing PBS treated sample2 The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample kidneys For determination of the host immune response induced by mRNA vaccine therapeutic adult zebrafish AB strain 3 to 4 mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5μg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer’s instructions. The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co. Ltd. Qingdao China and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature ∼28°C pH ∼7.4 and conductivity ∼1500μS. tissue:kidneys|cell type:whole cell immune cell|group:PBS treated group|treatment:2 dose of PBS immunized GSM8334552 GSM8334552: PBS treated sample2; Danio rerio; RNA Seq GSM8334552 r1 GSM8334552 1 post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP514436     PBS2.R2.fq.gz PBS2.R1.fq.gz fastq fastq 6919699470.0 23450956.0 GSM8334552 r1 0:147.53 1:147.54 A:1796088883;C:1654995114;G:1672062487;T:1796386928;N:166058 147 147     1796088883 1654995114 1672062487 1796386928 166058 SRX24954073 SRS21657731 SRA1905347 Zhang Lab, Department of Microbiology, Fudan University Zhang Lab, Department of Microbiology, Fudan University 2 0.9461 0.94623 0.06022 0.06009 0.70029 0.70017 0.51507 0.50298 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-06-17 Adult Adult Kidney Renal System
32793 32793 SRR29441661 SRX24954072 SRS21657730 SRP514436 PRJNA1125004 A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy GSE270105 Transcriptome Analysis Effective vaccines are urgently needed for the control of tuberculosis TB. Here we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB. Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity but not the canonical DNA damage responses that promote cell death demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably the mRNA vaccine induced autophagy in granulomas coinciding with bacterial killing and cell survival. Collectively these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control PBS control and untreatment control infection 14 days as well as healthy control. Adult zebrafish AB strain 3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5µg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before tr…   pubmed:39759874   PBS treated sample1 GSM8334551   source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:PBS treated group|treatment:2 dose of PBS immunized|geo loc name:missing|collection date:missing PBS treated sample1 The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample kidneys For determination of the host immune response induced by mRNA vaccine therapeutic adult zebrafish AB strain 3 to 4 mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5μg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer’s instructions. The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co. Ltd. Qingdao China and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature ∼28°C pH ∼7.4 and conductivity ∼1500μS. tissue:kidneys|cell type:whole cell immune cell|group:PBS treated group|treatment:2 dose of PBS immunized GSM8334551 GSM8334551: PBS treated sample1; Danio rerio; RNA Seq GSM8334551 r1 GSM8334551 1 post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP514436     PBS1.R1.fq.gz PBS1.R2.fq.gz fastq fastq 6655764529.0 22519009.0 GSM8334551 r1 0:147.78 1:147.78 A:1714166803;C:1603814821;G:1622004265;T:1715617121;N:161519 147 147     1714166803 1603814821 1622004265 1715617121 161519 SRX24954072 SRS21657730 SRA1905347 Zhang Lab, Department of Microbiology, Fudan University Zhang Lab, Department of Microbiology, Fudan University 2 0.946 0.94657 0.06234 0.06258 0.69558 0.69548 0.51124 0.51042 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-06-17 Adult Adult Kidney Renal System
32794 32794 SRR29441662 SRX24954071 SRS21657729 SRP514436 PRJNA1125004 A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy GSE270105 Transcriptome Analysis Effective vaccines are urgently needed for the control of tuberculosis TB. Here we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB. Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity but not the canonical DNA damage responses that promote cell death demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably the mRNA vaccine induced autophagy in granulomas coinciding with bacterial killing and cell survival. Collectively these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control PBS control and untreatment control infection 14 days as well as healthy control. Adult zebrafish AB strain 3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5µg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before tr…   pubmed:39759874   LPP treated sample3 GSM8334550   source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:Vector control treated group|treatment:2 dose of LPP GFP mRNA immunized|geo loc name:missing|collection date:missing LPP treated sample3 The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample kidneys For determination of the host immune response induced by mRNA vaccine therapeutic adult zebrafish AB strain 3 to 4 mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5μg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer’s instructions. The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co. Ltd. Qingdao China and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature ∼28°C pH ∼7.4 and conductivity ∼1500μS. tissue:kidneys|cell type:whole cell immune cell|group:Vector control treated group|treatment:2 dose of LPP GFP mRNA immunized GSM8334550 GSM8334550: LPP treated sample3; Danio rerio; RNA Seq GSM8334550 r1 GSM8334550 1 post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP514436     LPP3.R2.fq.gz LPP3.R1.fq.gz fastq fastq 6960795416.0 23521350.0 GSM8334550 r1 0:147.96 1:147.97 A:1794863170;C:1675740682;G:1695061647;T:1794948614;N:181303 147 147     1794863170 1675740682 1695061647 1794948614 181303 SRX24954071 SRS21657729 SRA1905347 Zhang Lab, Department of Microbiology, Fudan University Zhang Lab, Department of Microbiology, Fudan University 2 0.94576 0.94611 0.05967 0.05967 0.71116 0.71068 0.51094 0.50281 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-06-17 Adult Adult Kidney Renal System
32795 32795 SRR29441663 SRX24954070 SRS21657728 SRP514436 PRJNA1125004 A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy GSE270105 Transcriptome Analysis Effective vaccines are urgently needed for the control of tuberculosis TB. Here we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB. Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity but not the canonical DNA damage responses that promote cell death demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably the mRNA vaccine induced autophagy in granulomas coinciding with bacterial killing and cell survival. Collectively these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control PBS control and untreatment control infection 14 days as well as healthy control. Adult zebrafish AB strain 3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5µg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before tr…   pubmed:39759874   LPP treated sample2 GSM8334549   source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:Vector control treated group|treatment:2 dose of LPP GFP mRNA immunized|geo loc name:missing|collection date:missing LPP treated sample2 The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample kidneys For determination of the host immune response induced by mRNA vaccine therapeutic adult zebrafish AB strain 3 to 4 mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5μg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer’s instructions. The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co. Ltd. Qingdao China and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature ∼28°C pH ∼7.4 and conductivity ∼1500μS. tissue:kidneys|cell type:whole cell immune cell|group:Vector control treated group|treatment:2 dose of LPP GFP mRNA immunized GSM8334549 GSM8334549: LPP treated sample2; Danio rerio; RNA Seq GSM8334549 r1 GSM8334549 1 post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP514436     LPP2.R1.fq.gz LPP2.R2.fq.gz fastq fastq 6995236493.0 23852541.0 GSM8334549 r1 0:146.63 1:146.64 A:1801247979;C:1688505572;G:1704475825;T:1800830679;N:176438 146 146     1801247979 1688505572 1704475825 1800830679 176438 SRX24954070 SRS21657728 SRA1905347 Zhang Lab, Department of Microbiology, Fudan University Zhang Lab, Department of Microbiology, Fudan University 2 0.946 0.94652 0.0561 0.05623 0.70358 0.70366 0.52017 0.51073 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-06-17 Adult Adult Kidney Renal System
32796 32796 SRR29441664 SRX24954069 SRS21657726 SRP514436 PRJNA1125004 A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy GSE270105 Transcriptome Analysis Effective vaccines are urgently needed for the control of tuberculosis TB. Here we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB. Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity but not the canonical DNA damage responses that promote cell death demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably the mRNA vaccine induced autophagy in granulomas coinciding with bacterial killing and cell survival. Collectively these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control PBS control and untreatment control infection 14 days as well as healthy control. Adult zebrafish AB strain 3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5µg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before tr…   pubmed:39759874   LPP treated sample1 GSM8334548   source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:Vector control treated group|treatment:2 dose of LPP GFP mRNA immunized|geo loc name:missing|collection date:missing LPP treated sample1 The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample kidneys For determination of the host immune response induced by mRNA vaccine therapeutic adult zebrafish AB strain 3 to 4 mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5μg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer’s instructions. The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co. Ltd. Qingdao China and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature ∼28°C pH ∼7.4 and conductivity ∼1500μS. tissue:kidneys|cell type:whole cell immune cell|group:Vector control treated group|treatment:2 dose of LPP GFP mRNA immunized GSM8334548 GSM8334548: LPP treated sample1; Danio rerio; RNA Seq GSM8334548 r1 GSM8334548 1 post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP514436     LPP1.R2.fq.gz LPP1.R1.fq.gz fastq fastq 6929011698.0 23415693.0 GSM8334548 r1 0:147.95 1:147.96 A:1800504335;C:1654697874;G:1672501459;T:1801139766;N:168264 147 147     1800504335 1654697874 1672501459 1801139766 168264 SRX24954069 SRS21657726 SRA1905347 Zhang Lab, Department of Microbiology, Fudan University Zhang Lab, Department of Microbiology, Fudan University 2 0.94635 0.9465 0.05964 0.05918 0.71151 0.71121 0.51212 0.51768 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-06-17 Adult Adult Kidney Renal System
32797 32797 SRR29441665 SRX24954068 SRS21657724 SRP514436 PRJNA1125004 A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy GSE270105 Transcriptome Analysis Effective vaccines are urgently needed for the control of tuberculosis TB. Here we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB. Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity but not the canonical DNA damage responses that promote cell death demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably the mRNA vaccine induced autophagy in granulomas coinciding with bacterial killing and cell survival. Collectively these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control PBS control and untreatment control infection 14 days as well as healthy control. Adult zebrafish AB strain 3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5µg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before tr…   pubmed:39759874   L3T treated sample3 GSM8334547   source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:L3T treated group|treatment:2 dose of L3T mRNA immunized|geo loc name:missing|collection date:missing L3T treated sample3 The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample kidneys For determination of the host immune response induced by mRNA vaccine therapeutic adult zebrafish AB strain 3 to 4 mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5μg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer’s instructions. The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co. Ltd. Qingdao China and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature ∼28°C pH ∼7.4 and conductivity ∼1500μS. tissue:kidneys|cell type:whole cell immune cell|group:L3T treated group|treatment:2 dose of L3T mRNA immunized GSM8334547 GSM8334547: L3T treated sample3; Danio rerio; RNA Seq GSM8334547 r1 GSM8334547 1 post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP514436     L3T3.R2.fq.gz L3T3.R1.fq.gz fastq fastq 7001083805.0 23754500.0 GSM8334547 r1 0:147.36 1:147.37 A:1812658982;C:1679795926;G:1696938100;T:1811517827;N:172970 147 147     1812658982 1679795926 1696938100 1811517827 172970 SRX24954068 SRS21657724 SRA1905347 Zhang Lab, Department of Microbiology, Fudan University Zhang Lab, Department of Microbiology, Fudan University 2 0.94456 0.94488 0.05931 0.05871 0.70112 0.70035 0.49966 0.50266 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-06-17 Adult Adult Kidney Renal System
32798 32798 SRR29441666 SRX24954067 SRS21657727 SRP514436 PRJNA1125004 A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy GSE270105 Transcriptome Analysis Effective vaccines are urgently needed for the control of tuberculosis TB. Here we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB. Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity but not the canonical DNA damage responses that promote cell death demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably the mRNA vaccine induced autophagy in granulomas coinciding with bacterial killing and cell survival. Collectively these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control PBS control and untreatment control infection 14 days as well as healthy control. Adult zebrafish AB strain 3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5µg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before tr…   pubmed:39759874   L3T treated sample2 GSM8334546   source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:L3T treated group|treatment:2 dose of L3T mRNA immunized|geo loc name:missing|collection date:missing L3T treated sample2 The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample kidneys For determination of the host immune response induced by mRNA vaccine therapeutic adult zebrafish AB strain 3 to 4 mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5μg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer’s instructions. The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co. Ltd. Qingdao China and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature ∼28°C pH ∼7.4 and conductivity ∼1500μS. tissue:kidneys|cell type:whole cell immune cell|group:L3T treated group|treatment:2 dose of L3T mRNA immunized GSM8334546 GSM8334546: L3T treated sample2; Danio rerio; RNA Seq GSM8334546 r1 GSM8334546 1 post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP514436     L3T2.R2.fq.gz L3T2.R1.fq.gz fastq fastq 7045440387.0 23900950.0 GSM8334546 r1 0:147.38 1:147.39 A:1809443747;C:1705557966;G:1721919646;T:1808345574;N:173454 147 147     1809443747 1705557966 1721919646 1808345574 173454 SRX24954067 SRS21657727 SRA1905347 Zhang Lab, Department of Microbiology, Fudan University Zhang Lab, Department of Microbiology, Fudan University 2 0.94629 0.94712 0.05505 0.05485 0.69753 0.69654 0.50587 0.50695 131 131 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-06-17 Adult Adult Kidney Renal System
32799 32799 SRR29441667 SRX24954066 SRS21657725 SRP514436 PRJNA1125004 A mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy GSE270105 Transcriptome Analysis Effective vaccines are urgently needed for the control of tuberculosis TB. Here we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB. Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity but not the canonical DNA damage responses that promote cell death demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably the mRNA vaccine induced autophagy in granulomas coinciding with bacterial killing and cell survival. Collectively these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune therapeutic mechanisms mediated by the L3T vaccine we performed RNA seq analysis of kidneys isolated from Mycobacterium marinum infected zebrafish treatment with theL3T mRNA vaccine and the LPP control PBS control and untreatment control infection 14 days as well as healthy control. Adult zebrafish AB strain 3 to 4?mpf were infected with indicated M. marinum M strain for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5µg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before tr…   pubmed:39759874   L3T treated sample1 GSM8334545   source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:L3T treated group|treatment:2 dose of L3T mRNA immunized|geo loc name:missing|collection date:missing L3T treated sample1 The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes raw coutns for each Sample Supplementary files format and content: Tab delimited text files includes FPKM coutns for each Sample kidneys For determination of the host immune response induced by mRNA vaccine therapeutic adult zebrafish AB strain 3 to 4 mpf were infected with indicated M. marinum M strain about 50 100 CFU per fish for two weeks and were then injected twice with 3 day intervals day 14 and 17 of the L3T mRNA 0.5μg at the dorsal muscle using PV830 Pneumatic PicoPump microinjector and negative control zebrafish were immunized with LPP GFP mRNA or sterile PBS. post 7 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. We also collected the zebrafish kidneys infected with M. marinum M strain 14 days before treatment to RNA seq as mock named as M.m infection group and healthy kidneys as blank control named as Blank group. post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer’s instructions. The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co. Ltd. Qingdao China and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature ∼28°C pH ∼7.4 and conductivity ∼1500μS. tissue:kidneys|cell type:whole cell immune cell|group:L3T treated group|treatment:2 dose of L3T mRNA immunized GSM8334545 GSM8334545: L3T treated sample1; Danio rerio; RNA Seq GSM8334545 r1 GSM8334545 1 post 7 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP514436     L3T1.R1.fq.gz L3T1.R2.fq.gz fastq fastq 7005817977.0 23717988.0 GSM8334545 r1 0:147.68 1:147.70 A:1802621490;C:1692580332;G:1709393477;T:1801045146;N:177532 147 147     1802621490 1692580332 1709393477 1801045146 177532 SRX24954066 SRS21657725 SRA1905347 Zhang Lab, Department of Microbiology, Fudan University Zhang Lab, Department of Microbiology, Fudan University 2 0.94218 0.94275 0.05735 0.05684 0.69436 0.69325 0.5057 0.50501 134 134 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-06-17 Adult Adult Kidney Renal System
33649 33649 SRR30353607 SRX25811748 SRS22442019 SRP528282 PRJNA1151637 Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [scRNA seq] GSE275537 Transcriptome Analysis Single cell transcriptome analyses of whole kidney marrow cells isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: Single Cell RNA sequencing on whole kidney marrow cells isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171 which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. Single cell RNA sequencing was carried out in duplicates and each replicate consisted of cells dissociated from a pool of 2 4 adult whole kidney marrow.   pubmed:39548947   Rad21het rep2 GSM8479120   source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:rad21+/ |geo loc name:missing|collection date:missing Rad21het rep2 Fastq files were aligned to the Danio Rerio GRCz11 genome NCBI:GCA 000002035.4 using CellRanger version 6.0.1 with chemistry mode: SC3Pv3. Gene annotation came from Ensembl version 98. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: Tab seperated barcodes features and matrix files Whole kidney marrow   Fresh whole kidney marrow tissue was isolated from adult zebrafish and dissociated manually in PBS 5% fetal bovine serum solution and filtered through a 30 µm filter. Cells were counted using trypan blue and required cells were resuspended in PBS 0.04% bovine serum albumin solution. Single cells were isolated using the 10x genomics microfluidics system. Libraries were prepared using 3′ GEM library and Gel bead Kit v3.1 10x Genomics.   tissue:Whole kidney marrow|genotype:rad21+/ GSM8479120 GSM8479120: Rad21het rep2; Danio rerio; RNA Seq GSM8479120 r1 GSM8479120 1 Fresh whole kidney marrow tissue was isolated from adult zebrafish and dissociated manually in PBS 5% fetal bovine serum solution and filtered through a 30 µm filter. Cells were counted using trypan blue and required cells were resuspended in PBS 0.04% bovine serum albumin solution. Single cells were isolated using the 10x genomics microfluidics system. Libraries were prepared using 3′ GEM library and Gel bead Kit v3.1 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP528282     Rad21het_rep2_S1_L001_R2_001.fastq.gz Rad21het_rep2_S1_L001_R1_001.fastq.gz fastq fastq 25307099168.0 218164648.0 GSM8479120 r1 0:27 1:89 A:6829044594;C:5976366733;G:6024781695;T:6476303884;N:602262 27 89     6829044594 5976366733 6024781695 6476303884 602262 SRX25811748 SRS22442019 SRA1954153 Horsfield, Pathology, University of Otago Horsfield, Pathology, University of Otago 2 0.00381 0.89166 0.00123 0.07968 0.99279 0.82956 0.36032 0.51023 27 89 T B sc-like readlen illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   New Zealand 2024-08-23 Adult Adult Kidney Renal System
33650 33650 SRR30353608 SRX25811747 SRS22442018 SRP528282 PRJNA1151637 Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [scRNA seq] GSE275537 Transcriptome Analysis Single cell transcriptome analyses of whole kidney marrow cells isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: Single Cell RNA sequencing on whole kidney marrow cells isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171 which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. Single cell RNA sequencing was carried out in duplicates and each replicate consisted of cells dissociated from a pool of 2 4 adult whole kidney marrow.   pubmed:39548947   Rad21het rep1 GSM8479119   source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:rad21+/ |geo loc name:missing|collection date:missing Rad21het rep1 Fastq files were aligned to the Danio Rerio GRCz11 genome NCBI:GCA 000002035.4 using CellRanger version 6.0.1 with chemistry mode: SC3Pv3. Gene annotation came from Ensembl version 98. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: Tab seperated barcodes features and matrix files Whole kidney marrow   Fresh whole kidney marrow tissue was isolated from adult zebrafish and dissociated manually in PBS 5% fetal bovine serum solution and filtered through a 30 µm filter. Cells were counted using trypan blue and required cells were resuspended in PBS 0.04% bovine serum albumin solution. Single cells were isolated using the 10x genomics microfluidics system. Libraries were prepared using 3′ GEM library and Gel bead Kit v3.1 10x Genomics.   tissue:Whole kidney marrow|genotype:rad21+/ GSM8479119 GSM8479119: Rad21het rep1; Danio rerio; RNA Seq GSM8479119 r1 GSM8479119 1 Fresh whole kidney marrow tissue was isolated from adult zebrafish and dissociated manually in PBS 5% fetal bovine serum solution and filtered through a 30 µm filter. Cells were counted using trypan blue and required cells were resuspended in PBS 0.04% bovine serum albumin solution. Single cells were isolated using the 10x genomics microfluidics system. Libraries were prepared using 3′ GEM library and Gel bead Kit v3.1 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP528282     Rad21het_rep1_S1_L001_R2_001.fastq.gz Rad21het_rep1_S1_L001_R1_001.fastq.gz fastq fastq 22413519188.0 193219993.0 GSM8479119 r1 0:27 1:89 A:6260052051;C:5058503439;G:5315821015;T:5778634222;N:508461 27 89     6260052051 5058503439 5315821015 5778634222 508461 SRX25811747 SRS22442018 SRA1954153 Horsfield, Pathology, University of Otago Horsfield, Pathology, University of Otago 2 0.00394 0.90508 0.00119 0.09071 0.99162 0.82942 0.3619 0.54526 27 89 T B sc-like readlen illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   New Zealand 2024-08-23 Adult Adult Kidney Renal System
33651 33651 SRR30353609 SRX25811746 SRS22442017 SRP528282 PRJNA1151637 Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [scRNA seq] GSE275537 Transcriptome Analysis Single cell transcriptome analyses of whole kidney marrow cells isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: Single Cell RNA sequencing on whole kidney marrow cells isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171 which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. Single cell RNA sequencing was carried out in duplicates and each replicate consisted of cells dissociated from a pool of 2 4 adult whole kidney marrow.   pubmed:39548947   WT rep2 GSM8479118   source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:wild type|geo loc name:missing|collection date:missing WT rep2 Fastq files were aligned to the Danio Rerio GRCz11 genome NCBI:GCA 000002035.4 using CellRanger version 6.0.1 with chemistry mode: SC3Pv3. Gene annotation came from Ensembl version 98. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: Tab seperated barcodes features and matrix files Whole kidney marrow   Fresh whole kidney marrow tissue was isolated from adult zebrafish and dissociated manually in PBS 5% fetal bovine serum solution and filtered through a 30 µm filter. Cells were counted using trypan blue and required cells were resuspended in PBS 0.04% bovine serum albumin solution. Single cells were isolated using the 10x genomics microfluidics system. Libraries were prepared using 3′ GEM library and Gel bead Kit v3.1 10x Genomics.   tissue:Whole kidney marrow|genotype:wild type GSM8479118 GSM8479118: WT rep2; Danio rerio; RNA Seq GSM8479118 r1 GSM8479118 1 Fresh whole kidney marrow tissue was isolated from adult zebrafish and dissociated manually in PBS 5% fetal bovine serum solution and filtered through a 30 µm filter. Cells were counted using trypan blue and required cells were resuspended in PBS 0.04% bovine serum albumin solution. Single cells were isolated using the 10x genomics microfluidics system. Libraries were prepared using 3′ GEM library and Gel bead Kit v3.1 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP528282     WT_rep2_S1_L001_R1_001.fastq.gz WT_rep2_S1_L001_R2_001.fastq.gz fastq fastq 23457592964.0 202220629.0 GSM8479118 r1 0:27 1:89 A:6426793246;C:5417323760;G:5551103780;T:6061805923;N:566255 27 89     6426793246 5417323760 5551103780 6061805923 566255 SRX25811746 SRS22442017 SRA1954153 Horsfield, Pathology, University of Otago Horsfield, Pathology, University of Otago 2 0.00406 0.91487 0.00142 0.09007 0.99283 0.82641 0.37549 0.51858 27 89 T B sc-like readlen illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   New Zealand 2024-08-23 Adult Adult Kidney Renal System
33652 33652 SRR30353610 SRX25811745 SRS22442016 SRP528282 PRJNA1151637 Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [scRNA seq] GSE275537 Transcriptome Analysis Single cell transcriptome analyses of whole kidney marrow cells isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: Single Cell RNA sequencing on whole kidney marrow cells isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171 which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. Single cell RNA sequencing was carried out in duplicates and each replicate consisted of cells dissociated from a pool of 2 4 adult whole kidney marrow.   pubmed:39548947   WT rep1 GSM8479117   source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:wild type|geo loc name:missing|collection date:missing WT rep1 Fastq files were aligned to the Danio Rerio GRCz11 genome NCBI:GCA 000002035.4 using CellRanger version 6.0.1 with chemistry mode: SC3Pv3. Gene annotation came from Ensembl version 98. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: Tab seperated barcodes features and matrix files Whole kidney marrow   Fresh whole kidney marrow tissue was isolated from adult zebrafish and dissociated manually in PBS 5% fetal bovine serum solution and filtered through a 30 µm filter. Cells were counted using trypan blue and required cells were resuspended in PBS 0.04% bovine serum albumin solution. Single cells were isolated using the 10x genomics microfluidics system. Libraries were prepared using 3′ GEM library and Gel bead Kit v3.1 10x Genomics.   tissue:Whole kidney marrow|genotype:wild type GSM8479117 GSM8479117: WT rep1; Danio rerio; RNA Seq GSM8479117 r1 GSM8479117 1 Fresh whole kidney marrow tissue was isolated from adult zebrafish and dissociated manually in PBS 5% fetal bovine serum solution and filtered through a 30 µm filter. Cells were counted using trypan blue and required cells were resuspended in PBS 0.04% bovine serum albumin solution. Single cells were isolated using the 10x genomics microfluidics system. Libraries were prepared using 3′ GEM library and Gel bead Kit v3.1 10x Genomics.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP528282     WT_rep1_S1_L001_R2_001.fastq.gz WT_rep1_S1_L001_R1_001.fastq.gz fastq fastq 26909031908.0 231974413.0 GSM8479117 r1 0:27 1:89 A:7272478752;C:6312728360;G:6433038501;T:6890198195;N:588100 27 89     7272478752 6312728360 6433038501 6890198195 588100 SRX25811745 SRS22442016 SRA1954153 Horsfield, Pathology, University of Otago Horsfield, Pathology, University of Otago 2 0.00366 0.93902 0.00134 0.0858 0.99318 0.82769 0.35 0.51885 27 89 T B sc-like readlen illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   New Zealand 2024-08-23 Adult Adult Kidney Renal System
33653 33653 SRR30355362 SRX25813460 SRS22443728 SRP528295 PRJNA1151638 Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [bulkRNA seq] GSE275536 Transcriptome Analysis Bulk RNA sequencing analyses of whole kidney marrow tissue isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: RNA sequencing was carried out on whole kidney marrow tissue isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171 which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. RNA sequencing was carried out in triplicates and each replicate consisted of whole kidney marrow pooled from three adult zebrafish.   pubmed:39548947   Rad21het rep3 GSM8479116   source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:rad21+/ |geo loc name:missing|collection date:missing Rad21het rep3 Sequencing reads were QC using FastQC. Sequencing adapter and low quality Q<20 were removed using fastq mcf. Cleaned reads were aligned using HISAT2 version 2.0.4. Read count were retrieved using FeatureCount summarising data at gene id level. Transcript per milion were generated using featureCount read count using R. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: tab delimited text file contains the transcript parts million countsTPM for each sample Whole kidney marrow   Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq® RNA Sample Preparation v2   tissue:Whole kidney marrow|genotype:rad21+/ GSM8479116 GSM8479116: Rad21het rep3; Danio rerio; RNA Seq GSM8479116 r1 GSM8479116 1 Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq® RNA Sample Preparation v2   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Five   SRP528295     Rad21het_rep3_L001_R1_001.fastq.gz Rad21het_rep3_L001_R2_001.fastq.gz fastq fastq 11739699756.0 38873178.0 GSM8479116 r1 0:151 1:151 A:3023039412;C:2849320583;G:2949255547;T:2917120212;N:964002 151 151     3023039412 2849320583 2949255547 2917120212 964002 SRX25813460 SRS22443728 SRA1954177 Horsfield, Pathology, University of Otago Horsfield, Pathology, University of Otago 2 0.91949 0.91921 0.02856 0.02841 0.72287 0.72969 0.50988 0.50739 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   New Zealand 2024-08-23 Adult Adult Kidney Renal System
33654 33654 SRR30355363 SRX25813459 SRS22443727 SRP528295 PRJNA1151638 Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [bulkRNA seq] GSE275536 Transcriptome Analysis Bulk RNA sequencing analyses of whole kidney marrow tissue isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: RNA sequencing was carried out on whole kidney marrow tissue isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171 which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. RNA sequencing was carried out in triplicates and each replicate consisted of whole kidney marrow pooled from three adult zebrafish.   pubmed:39548947   Rad21het rep2 GSM8479115   source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:rad21+/ |geo loc name:missing|collection date:missing Rad21het rep2 Sequencing reads were QC using FastQC. Sequencing adapter and low quality Q<20 were removed using fastq mcf. Cleaned reads were aligned using HISAT2 version 2.0.4. Read count were retrieved using FeatureCount summarising data at gene id level. Transcript per milion were generated using featureCount read count using R. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: tab delimited text file contains the transcript parts million countsTPM for each sample Whole kidney marrow   Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq® RNA Sample Preparation v2   tissue:Whole kidney marrow|genotype:rad21+/ GSM8479115 GSM8479115: Rad21het rep2; Danio rerio; RNA Seq GSM8479115 r1 GSM8479115 1 Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq® RNA Sample Preparation v2   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Five   SRP528295     Rad21het_rep2_L001_R1_001.fastq.gz Rad21het_rep2_L001_R2_001.fastq.gz fastq fastq 15263700610.0 50542055.0 GSM8479115 r1 0:151 1:151 A:3934169632;C:3701506984;G:3857649812;T:3769115522;N:1258660 151 151     3934169632 3701506984 3857649812 3769115522 1258660 SRX25813459 SRS22443727 SRA1954177 Horsfield, Pathology, University of Otago Horsfield, Pathology, University of Otago 2 0.9227 0.92195 0.02689 0.02669 0.72547 0.73196 0.47904 0.48582 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   New Zealand 2024-08-23 Adult Adult Kidney Renal System
33655 33655 SRR30355364 SRX25813458 SRS22443726 SRP528295 PRJNA1151638 Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [bulkRNA seq] GSE275536 Transcriptome Analysis Bulk RNA sequencing analyses of whole kidney marrow tissue isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: RNA sequencing was carried out on whole kidney marrow tissue isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171 which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. RNA sequencing was carried out in triplicates and each replicate consisted of whole kidney marrow pooled from three adult zebrafish.   pubmed:39548947   Rad21het rep1 GSM8479114   source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:rad21+/ |geo loc name:missing|collection date:missing Rad21het rep1 Sequencing reads were QC using FastQC. Sequencing adapter and low quality Q<20 were removed using fastq mcf. Cleaned reads were aligned using HISAT2 version 2.0.4. Read count were retrieved using FeatureCount summarising data at gene id level. Transcript per milion were generated using featureCount read count using R. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: tab delimited text file contains the transcript parts million countsTPM for each sample Whole kidney marrow   Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq® RNA Sample Preparation v2   tissue:Whole kidney marrow|genotype:rad21+/ GSM8479114 GSM8479114: Rad21het rep1; Danio rerio; RNA Seq GSM8479114 r1 GSM8479114 1 Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq® RNA Sample Preparation v2   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Five   SRP528295     Rad21het_rep1_L001_R1_001.fastq.gz Rad21het_rep1_L001_R2_001.fastq.gz fastq fastq 12383733782.0 41005741.0 GSM8479114 r1 0:151 1:151 A:3185412651;C:3011130011;G:3135728222;T:3050446997;N:1015901 151 151     3185412651 3011130011 3135728222 3050446997 1015901 SRX25813458 SRS22443726 SRA1954177 Horsfield, Pathology, University of Otago Horsfield, Pathology, University of Otago 2 0.9242 0.92383 0.0273 0.02728 0.72151 0.72683 0.47619 0.48803 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   New Zealand 2024-08-23 Adult Adult Kidney Renal System
33656 33656 SRR30355365 SRX25813457 SRS22443744 SRP528295 PRJNA1151638 Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [bulkRNA seq] GSE275536 Transcriptome Analysis Bulk RNA sequencing analyses of whole kidney marrow tissue isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: RNA sequencing was carried out on whole kidney marrow tissue isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171 which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. RNA sequencing was carried out in triplicates and each replicate consisted of whole kidney marrow pooled from three adult zebrafish.   pubmed:39548947   WT rep3 GSM8479113   source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:wild type|geo loc name:missing|collection date:missing WT rep3 Sequencing reads were QC using FastQC. Sequencing adapter and low quality Q<20 were removed using fastq mcf. Cleaned reads were aligned using HISAT2 version 2.0.4. Read count were retrieved using FeatureCount summarising data at gene id level. Transcript per milion were generated using featureCount read count using R. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: tab delimited text file contains the transcript parts million countsTPM for each sample Whole kidney marrow   Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq® RNA Sample Preparation v2   tissue:Whole kidney marrow|genotype:wild type GSM8479113 GSM8479113: WT rep3; Danio rerio; RNA Seq GSM8479113 r1 GSM8479113 1 Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq® RNA Sample Preparation v2   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Five   SRP528295     WT_rep3_L001_R1_001.fastq.gz WT_rep3_L001_R2_001.fastq.gz fastq fastq 13242216498.0 43848399.0 GSM8479113 r1 0:151 1:151 A:3400902046;C:3224156106;G:3363313174;T:3252754642;N:1090530 151 151     3400902046 3224156106 3363313174 3252754642 1090530 SRX25813457 SRS22443744 SRA1954177 Horsfield, Pathology, University of Otago Horsfield, Pathology, University of Otago 2 0.91607 0.91443 0.02817 0.02789 0.705 0.7107 0.51363 0.49767 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   New Zealand 2024-08-23 Adult Adult Kidney Renal System
33657 33657 SRR30355366 SRX25813456 SRS22443725 SRP528295 PRJNA1151638 Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [bulkRNA seq] GSE275536 Transcriptome Analysis Bulk RNA sequencing analyses of whole kidney marrow tissue isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: RNA sequencing was carried out on whole kidney marrow tissue isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171 which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. RNA sequencing was carried out in triplicates and each replicate consisted of whole kidney marrow pooled from three adult zebrafish.   pubmed:39548947   WT rep2 GSM8479112   source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:wild type|geo loc name:missing|collection date:missing WT rep2 Sequencing reads were QC using FastQC. Sequencing adapter and low quality Q<20 were removed using fastq mcf. Cleaned reads were aligned using HISAT2 version 2.0.4. Read count were retrieved using FeatureCount summarising data at gene id level. Transcript per milion were generated using featureCount read count using R. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: tab delimited text file contains the transcript parts million countsTPM for each sample Whole kidney marrow   Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq® RNA Sample Preparation v2   tissue:Whole kidney marrow|genotype:wild type GSM8479112 GSM8479112: WT rep2; Danio rerio; RNA Seq GSM8479112 r1 GSM8479112 1 Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq® RNA Sample Preparation v2   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Five   SRP528295     WT_rep2_L001_R1_001.fastq.gz WT_rep2_L001_R2_001.fastq.gz fastq fastq 10248296614.0 33934757.0 GSM8479112 r1 0:151 1:151 A:2636593190;C:2486812997;G:2585808493;T:2538244274;N:837660 151 151     2636593190 2486812997 2585808493 2538244274 837660 SRX25813456 SRS22443725 SRA1954177 Horsfield, Pathology, University of Otago Horsfield, Pathology, University of Otago 2 0.91112 0.91075 0.02202 0.02161 0.70942 0.71719 0.47568 0.49773 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   New Zealand 2024-08-23 Adult Adult Kidney Renal System
33658 33658 SRR30355367 SRX25813455 SRS22443724 SRP528295 PRJNA1151638 Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [bulkRNA seq] GSE275536 Transcriptome Analysis Bulk RNA sequencing analyses of whole kidney marrow tissue isolated from wild type and rad21 heterozygous mutant adult zebrafish. Overall design: RNA sequencing was carried out on whole kidney marrow tissue isolated from adult zebrafish that were wild type or carry germline heterozygous mutation in the rad21 gene. The zebrafish rad21 allele used in this study was rad21nz171 which contains a nonsense mutation in exon 8 of the zebrafish rad21a gene converting a glycine to a stop codon. The wild type zebrafish utilized were the wild type siblings obtained from in cross of rad21 heterozygous mutant zebrafish. RNA sequencing was carried out in triplicates and each replicate consisted of whole kidney marrow pooled from three adult zebrafish.   pubmed:39548947   WT rep1 GSM8479111   source name:Whole kidney marrow|tissue:Whole kidney marrow|genotype:wild type|geo loc name:missing|collection date:missing WT rep1 Sequencing reads were QC using FastQC. Sequencing adapter and low quality Q<20 were removed using fastq mcf. Cleaned reads were aligned using HISAT2 version 2.0.4. Read count were retrieved using FeatureCount summarising data at gene id level. Transcript per milion were generated using featureCount read count using R. Assembly: Danio Rerio genome GRCz11 Supplementary files format and content: tab delimited text file contains the transcript parts million countsTPM for each sample Whole kidney marrow   Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq® RNA Sample Preparation v2   tissue:Whole kidney marrow|genotype:wild type GSM8479111 GSM8479111: WT rep1; Danio rerio; RNA Seq GSM8479111 r1 GSM8479111 1 Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit MACHEREY NAGEL. Libraries were prepared using the Illumina TruSeq® RNA Sample Preparation v2   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Five   SRP528295     WT_rep1_L001_R1_001.fastq.gz WT_rep1_L001_R2_001.fastq.gz fastq fastq 11368938584.0 37645492.0 GSM8479111 r1 0:151 1:151 A:2896983545;C:2796736516;G:2916252779;T:2758034822;N:930922 151 151     2896983545 2796736516 2916252779 2758034822 930922 SRX25813455 SRS22443724 SRA1954177 Horsfield, Pathology, University of Otago Horsfield, Pathology, University of Otago 2 0.91882 0.91785 0.02974 0.02968 0.72105 0.72693 0.50274 0.49954 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk bulk bulk   New Zealand 2024-08-23 Adult Adult Kidney Renal System
34960 34960 SRR32588717 SRX27895234 SRS24266236 SRP568323 PRJNA1232602 Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains PRJNA1232602 Other In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.       Iso Seq RNA from Danio rerio C2 F2 F K   strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:kidney|BioSampleModel:Model organism or animal                 Iso Seq RNA from kidney C2 F2 F K C2 F2 F K The long Read Sequencing libraries was sequenced using PacBio Sequel II     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel II   SRP568323     m84270_240904_132604_s1.skera.flnc.fastq.gz fastq 109258150145.0 61126158.0 m84270 240904 132604 s1.skera.flnc.fastq.gz 0:1787.42 A:32153042096;C:22604112467;G:23394852841;T:31106142741;N:0 1787       32153042096 22604112467 23394852841 31106142741 0 SRX27895234 SRS24266236 SRA2089085 National Human Genome Research Institute|Translational and Functional Genomics Branch National Human Genome Research Institute National Human Genome Research Institute                       T   long read pacbio pacbio_modern unknown cdna_unspecified unknown bulk unknown unknown   United States 2025-03-06 Adult Adult Kidney Renal System
34970 34970 SRR32588727 SRX27895224 SRS24266224 SRP568323 PRJNA1232602 Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains PRJNA1232602 Other In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.       Iso Seq RNA from Danio rerio C2 F2 M K22   strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:male|tissue:kidney|BioSampleModel:Model organism or animal                 Iso Seq RNA from kidney C2 F2 M K22 C2 F2 M K22 The long Read Sequencing libraries was sequenced using PacBio Sequel II     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel II   SRP568323     m64467e_240829_144745.hifi_reads.flnc.fastq.gz fastq 14838539048.0 3383142.0 m64467e 240829 144745.hifi reads.flnc.fastq.gz 0:4386.02 A:4211191682;C:3185079857;G:3320422646;T:4121844863;N:0 4386       4211191682 3185079857 3320422646 4121844863 0 SRX27895224 SRS24266224 SRA2089085 National Human Genome Research Institute|Translational and Functional Genomics Branch National Human Genome Research Institute National Human Genome Research Institute                       T   long read pacbio pacbio_modern unknown cdna_unspecified unknown bulk unknown unknown   United States 2025-03-06 Adult Adult Kidney Renal System
34971 34971 SRR32588728 SRX27895223 SRS24266234 SRP568323 PRJNA1232602 Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains PRJNA1232602 Other In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.       Iso Seq RNA from Danio rerio C2 F2 M K21   strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:male|tissue:Kidney|BioSampleModel:Model organism or animal                 Iso Seq RNA from kidney C2 F2 M K21 C2 F2 M K21 The long Read Sequencing libraries was sequenced using PacBio Sequel II     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel II   SRP568323     m84270_240913_170640_s3.skera.flnc.fastq.gz fastq 100849133955.0 51593887.0 m84270 240913 170640 s3.skera.flnc.fastq.gz 0:1954.67 A:28887816631;C:21568633305;G:22323254809;T:28069429210;N:0 1954       28887816631 21568633305 22323254809 28069429210 0 SRX27895223 SRS24266234 SRA2089085 National Human Genome Research Institute|Translational and Functional Genomics Branch National Human Genome Research Institute National Human Genome Research Institute                       T   long read pacbio pacbio_modern unknown cdna_unspecified unknown bulk unknown unknown   United States 2025-03-06 Adult Adult Kidney Renal System
38061 38061 SRR1524243 SRX661008 SRS665983 SRP044781 PRJNA255848 Danio rerio Transcriptome PRJNA255848 Transcriptome Analysis Transcriptome analysis of 12 zebrafish tissues parent bioproject:PRJNA255979 pubmed:27189481 Zebrafish Kidney Zebrafish Kidney F Dr 7   strain:AB|age:5 month|biomaterial provider:INRA|sex:male and female|tissue:Kidney|BioSampleModel:Model organism or animal                 Zebrafish Kidney F Dr 7 F Dr 7 Total RNA was qualified using an Agilent BioAnalyzer and 1 µg was used for polyA selection and library construction with Illumina's TruSeq stranded total RNA sample preparation kit according to the manufacturer's instructions TruSeq stranded total RNA SamplePrep Guide RevC     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP044781     F_Dr_7_TGACCA_L003_R2.fastq.gz F_Dr_7_TGACCA_L003_R1.fastq.gz fastq fastq 9274322800.0 46371614.0 F Dr 7 files 0:100 1:100 A:2454755033;C:2186725747;G:2191996485;T:2432936369;N:7909166 100 100     2454755033 2186725747 2191996485 2432936369 7909166 SRX661008 SRS665983 SRA176464 INRA|Fish Physiology and Genomics INRA PhyloFish 2 0.93261 0.92609 0.06804 0.06819 0.69757 0.69771 0.48358 0.49333 100 100 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   France 2015-07-24 Adult Adult Kidney Renal System
38266 38266 SRR1609749 SRX730402 SRS719623 SRP048807 PRJNA263496 Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish GSE62221 Transcriptome Analysis The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures ranging from normal 28°C to mild 18°C and severe 10°C cold using RNA seq. The tissues varied in the number of cold responsive genes of which the kidney appeared to be most sensitive whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes such as RNA splicing and proton transport as well tissue specific processes such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program DREME. Eleven motifs 6 known and 5 novel were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs such as the AP 1 and STAT1 binding sites are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures   pubmed:26227973   kidney10 GSM1523044   source name:kidney|tissue:kidney|temperature:10°C|strain:Tubingen|age:6 mpf kidney10 Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html which is a python based script was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... kidney fish were maintained 12h to adapt low temperatures and then killed by pithing Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:kidney|temperature:10°C|strain:Tubingen|age:6 mpf GSM1523044 GSM1523044: kidney10; Danio rerio; RNA Seq GSM1523044   1 Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1523044 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP048807     kidney10_1.fq.gz kidney10_2.fq.gz fastq fastq 4315071200.0 21575356.0 GSM1523044 r1 0:100 1:100 A:1152823680;C:1012018705;G:1003451232;T:1146696176;N:81407 100 100     1152823680 1012018705 1003451232 1146696176 81407 SRX730402 SRS719623 SRA189240 GEO Shanghai Ocean University 2 0.95345 0.94751 0.05494 0.05445 0.7455 0.74856 0.53555 0.52518 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   China 2014-10-09 Adult Adult Kidney Renal System
38267 38267 SRR1609748 SRX730401 SRS719622 SRP048807 PRJNA263496 Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish GSE62221 Transcriptome Analysis The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures ranging from normal 28°C to mild 18°C and severe 10°C cold using RNA seq. The tissues varied in the number of cold responsive genes of which the kidney appeared to be most sensitive whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes such as RNA splicing and proton transport as well tissue specific processes such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program DREME. Eleven motifs 6 known and 5 novel were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs such as the AP 1 and STAT1 binding sites are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures   pubmed:26227973   kidney18 GSM1523043   source name:kidney|tissue:kidney|temperature:18°C|strain:Tubingen|age:6 mpf kidney18 Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html which is a python based script was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... kidney fish were maintained 12h to adapt low temperatures and then killed by pithing Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:kidney|temperature:18°C|strain:Tubingen|age:6 mpf GSM1523043 GSM1523043: kidney18; Danio rerio; RNA Seq GSM1523043   1 Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1523043 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP048807     kidney18_1.fq.gz kidney18_2.fq.gz fastq fastq 3876913200.0 19384566.0 GSM1523043 r1 0:100 1:100 A:1015185474;C:927880228;G:918980502;T:1014805063;N:61933 100 100     1015185474 927880228 918980502 1014805063 61933 SRX730401 SRS719622 SRA189240 GEO Shanghai Ocean University 2 0.94462 0.93747 0.03424 0.03391 0.72243 0.7262 0.49704 0.4967 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   China 2014-10-09 Adult Adult Kidney Renal System
38268 38268 SRR1609747 SRX730400 SRS719621 SRP048807 PRJNA263496 Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish GSE62221 Transcriptome Analysis The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures ranging from normal 28°C to mild 18°C and severe 10°C cold using RNA seq. The tissues varied in the number of cold responsive genes of which the kidney appeared to be most sensitive whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes such as RNA splicing and proton transport as well tissue specific processes such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program DREME. Eleven motifs 6 known and 5 novel were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs such as the AP 1 and STAT1 binding sites are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures   pubmed:26227973   kidney28 GSM1523042   source name:kidney|tissue:kidney|temperature:28°C|strain:Tubingen|age:6 mpf kidney28 Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html which is a python based script was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... kidney fish were maintained 12h to adapt low temperatures and then killed by pithing Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:kidney|temperature:28°C|strain:Tubingen|age:6 mpf GSM1523042 GSM1523042: kidney28; Danio rerio; RNA Seq GSM1523042   1 Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1523042 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP048807     kidney28_1.fq.gz kidney28_2.fq.gz fastq fastq 4590135400.0 22950677.0 GSM1523042 r1 0:100 1:100 A:1216408799;C:1078601401;G:1076605621;T:1218430409;N:89170 100 100     1216408799 1078601401 1076605621 1218430409 89170 SRX730400 SRS719621 SRA189240 GEO Shanghai Ocean University 2 0.96555 0.9628 0.03027 0.03021 0.79015 0.79269 0.26504 0.27074 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   China 2014-10-09 Adult Adult Kidney Renal System
38296 38296 SRR1647681 SRX756916 SRS742120 SRP049663 PRJNA266803 Spring Varaemia of Carp Virus SVCV infection of adult zebrafish GSE63133 Transcriptome Analysis During viral infection a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection i.e. 6h and 24h post infection. For 12 zebrafish IRFs we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7 which together with DrIRF3 was highly induced by SVCV infection. For type I IFNs zebrafish has four IFN genes three of which IFN1/2/3 particularly IFN 1 and IFN 3 were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately 50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.   pubmed:25535281   24K GSM1541905   source name:head kidney|tissue:head kidney|disease state:24h post SVCV infection 24K Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... head kidney   Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:head kidney|disease state:24h post SVCV infection GSM1541905 GSM1541905: 24K; Danio rerio; RNA Seq GSM1541905   1 Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1541905 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP049663     24K_GTGAAA_L003_R1.fastq fastq 1020487560.0 20009560.0 GSM1541905 r1 0:51 A:266117014;C:246797067;G:240014464;T:267491299;N:67716 51       266117014 246797067 240014464 267491299 67716 SRX756916 SRS742120 SRA200717 GEO Institute of Hydrobiology, Chinese Academy of Sciences 1 0.92411   0.07686   0.68647   0.4627   51   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-11-10 Undetermined Adult Kidney Renal System
38297 38297 SRR1647680 SRX756915 SRS742117 SRP049663 PRJNA266803 Spring Varaemia of Carp Virus SVCV infection of adult zebrafish GSE63133 Transcriptome Analysis During viral infection a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection i.e. 6h and 24h post infection. For 12 zebrafish IRFs we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7 which together with DrIRF3 was highly induced by SVCV infection. For type I IFNs zebrafish has four IFN genes three of which IFN1/2/3 particularly IFN 1 and IFN 3 were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately 50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.   pubmed:25535281   6K GSM1541904   source name:head kidney|tissue:head kidney|disease state:6h post SVCV infection 6K Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... head kidney   Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:head kidney|disease state:6h post SVCV infection GSM1541904 GSM1541904: 6K; Danio rerio; RNA Seq GSM1541904   1 Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1541904 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP049663     6K_GTCCGC_L003_R1.fastq fastq 929436036.0 18224236.0 GSM1541904 r1 0:51 A:242005719;C:225485975;G:219890494;T:241993975;N:59873 51       242005719 225485975 219890494 241993975 59873 SRX756915 SRS742117 SRA200717 GEO Institute of Hydrobiology, Chinese Academy of Sciences 1 0.92547   0.09105   0.69264   0.49166   51   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-11-10 Undetermined Adult Kidney Renal System
38298 38298 SRR1647679 SRX756914 SRS742116 SRP049663 PRJNA266803 Spring Varaemia of Carp Virus SVCV infection of adult zebrafish GSE63133 Transcriptome Analysis During viral infection a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection i.e. 6h and 24h post infection. For 12 zebrafish IRFs we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7 which together with DrIRF3 was highly induced by SVCV infection. For type I IFNs zebrafish has four IFN genes three of which IFN1/2/3 particularly IFN 1 and IFN 3 were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately 50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.   pubmed:25535281   0K GSM1541903   source name:head kidney|tissue:head kidney|disease state:un infected 0K Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... head kidney   Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:head kidney|disease state:un infected GSM1541903 GSM1541903: 0K; Danio rerio; RNA Seq GSM1541903   1 Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1541903 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP049663     0K_CCGTCC_L003_R1.fastq fastq 1077979095.0 21136845.0 GSM1541903 r1 0:51 A:280277150;C:261348733;G:255721013;T:280562071;N:70128 51       280277150 261348733 255721013 280562071 70128 SRX756914 SRS742116 SRA200717 GEO Institute of Hydrobiology, Chinese Academy of Sciences 1 0.92545   0.08181   0.68373   0.49408   51   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-11-10 Undetermined Adult Kidney Renal System
41473 41473 SRR5457065 SRX2745133 SRS1761840 SRP092128 PRJNA350712 Phylogenetic analysis of intron retention in vertebrates PRJNA350712 Other Our study is detailing new evidence for transcriptomic complexity realized by a mechanism of orchestrated intron retention.       zebrafish granulocytes dre granulocytes   strain: |age:3 month 6 month|sex:male|tissue:kidney marrow|biomaterial provider:Graham Lieschke|cell type:granulocyte|health state:healthy|BioSampleModel:Model organism or animal                 RNAseq of zebrafish granulocytes dre gran TruSeq RNA paired Ill HiSeq2000 dre gran TruSeq RNA paired Ill HiSeq2000 RNA seq libraries were prepared from >1 g of total RNA using TruSeq RNA sample prep kit Illumina according to the manufacturersÍ instructions     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP092128     Zebrafish-1_ZF1_1.fastq.gz Zebrafish-1_ZF1_2.fastq.gz Zebrafish-1_ZF3_1.fastq.gz Zebrafish-1_ZF3_2.fastq.gz fastq fastq fastq fastq 27103033264.0 134173432.0 Zebrafish 1 ZF3 2.fastq.gz 0:101 1:101 A:7205178092;C:6377884075;G:6326441274;T:7192445241;N:1084582 101 101     7205178092 6377884075 6326441274 7192445241 1084582 SRX2745133 SRS1761840 SRA555068 Centenary Institute|Gene &amp; Stem Cell Therapy Program Centenary Institute 2 0.97153 0.98059 0.09216 0.09282 0.72679 0.7234 0.46875 0.47002 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Australia 2017-04-19 Adult Adult Kidney Renal System
41902 41902 SRR5337748 SRX2635098 SRS2043910 SRP101756 PRJNA378882 Transcriptome of the distal late segment of the zebrafish mesonephros GSE96519 Transcriptome Analysis We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.   pubmed:28656378   YS6 GSM2534771   tissue:Mes1phros DL|transgene:Tgslc12a3:mCherry|genotype:mCh |age:adult YS6 none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts Mesonephros DL   DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.   transgene:Tgslc12a3:mCherry|genotype:mCh |age:adult GSM2534771 GSM2534771: YS6; Danio rerio; RNA Seq GSM2534771   1 DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN. GEO Accession:GSM2534771 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP101756     20150717.A-YS6_R1.fastq.gz fastq 5434051896.0 43127396.0 GSM2534771 r1 0:126 A:1185876928;C:1354521221;G:1643633065;T:1249907593;N:113089 126       1185876928 1354521221 1643633065 1249907593 113089 SRX2635098 SRS2043910 SRA544882 GEO Drummond, Nephrology, Massachusetts General Hospital 1 0.97351   0.17501   0.85303   0.75625   126   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   United States 2017-03-12 Adult Adult Kidney Renal System
41903 41903 SRR5337747 SRX2635097 SRS2043909 SRP101756 PRJNA378882 Transcriptome of the distal late segment of the zebrafish mesonephros GSE96519 Transcriptome Analysis We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.   pubmed:28656378   YS5 GSM2534770   tissue:DL segments|transgene:Tgslc12a3:mCherry|genotype:mCh+|age:adult YS5 none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts DL segments   DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.   transgene:Tgslc12a3:mCherry|genotype:mCh+|age:adult GSM2534770 GSM2534770: YS5; Danio rerio; RNA Seq GSM2534770   1 DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN. GEO Accession:GSM2534770 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP101756     20150717.A-YS5_R1.fastq(1).gz fastq 2297696058.0 18235683.0 GSM2534770 r1 0:126 A:648837532;C:505738661;G:568578688;T:574489076;N:52101 126       648837532 505738661 568578688 574489076 52101 SRX2635097 SRS2043909 SRA544882 GEO Drummond, Nephrology, Massachusetts General Hospital 1 0.94402   0.1927   0.77585   0.67728   126   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   United States 2017-03-12 Adult Adult Kidney Renal System
41904 41904 SRR5337746 SRX2635096 SRS2043908 SRP101756 PRJNA378882 Transcriptome of the distal late segment of the zebrafish mesonephros GSE96519 Transcriptome Analysis We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.   pubmed:28656378   YS4 GSM2534769   tissue:Mes1phros DL|transgene:Tgslc12a3:mCherry|genotype:mCh |age:adult YS4 none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts Mesonephros DL   DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.   transgene:Tgslc12a3:mCherry|genotype:mCh |age:adult GSM2534769 GSM2534769: YS4; Danio rerio; RNA Seq GSM2534769   1 DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN. GEO Accession:GSM2534769 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP101756     20150717.A-YS4_R1.fastq.gz fastq 4570634754.0 36274879.0 GSM2534769 r1 0:126 A:1179398927;C:1024363944;G:1239125274;T:1127644877;N:101732 126       1179398927 1024363944 1239125274 1127644877 101732 SRX2635096 SRS2043908 SRA544882 GEO Drummond, Nephrology, Massachusetts General Hospital 1 0.93083   0.27465   0.78102   0.70638   126   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   United States 2017-03-12 Adult Adult Kidney Renal System
41905 41905 SRR5337745 SRX2635095 SRS2043907 SRP101756 PRJNA378882 Transcriptome of the distal late segment of the zebrafish mesonephros GSE96519 Transcriptome Analysis We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.   pubmed:28656378   YS3 GSM2534768   tissue:DL segments|transgene:Tgslc12a3:mCherry|genotype:mCh+|age:adult YS3 none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts DL segments   DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.   transgene:Tgslc12a3:mCherry|genotype:mCh+|age:adult GSM2534768 GSM2534768: YS3; Danio rerio; RNA Seq GSM2534768   1 DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN. GEO Accession:GSM2534768 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP101756     20150717.A-YS3_R1.fastq.gz fastq 5648398686.0 44828561.0 GSM2534768 r1 0:126 A:1607436982;C:1222995706;G:1369036558;T:1448805498;N:123942 126       1607436982 1222995706 1369036558 1448805498 123942 SRX2635095 SRS2043907 SRA544882 GEO Drummond, Nephrology, Massachusetts General Hospital 1 0.93399   0.20266   0.78076   0.73978   126   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   United States 2017-03-12 Adult Adult Kidney Renal System
41906 41906 SRR5337744 SRX2635094 SRS2043906 SRP101756 PRJNA378882 Transcriptome of the distal late segment of the zebrafish mesonephros GSE96519 Transcriptome Analysis We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.   pubmed:28656378   YS2 GSM2534767   tissue:Mes1phros DL|transgene:Tgslc12a3:mCherry|genotype:mCh |age:adult YS2 none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts Mesonephros DL   DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.   transgene:Tgslc12a3:mCherry|genotype:mCh |age:adult GSM2534767 GSM2534767: YS2; Danio rerio; RNA Seq GSM2534767   1 DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN. GEO Accession:GSM2534767 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP101756     20150717.A-YS2_R1.fastq.gz fastq 4680679374.0 37148249.0 GSM2534767 r1 0:126 A:1320151433;C:986429614;G:1112497899;T:1261495719;N:104709 126       1320151433 986429614 1112497899 1261495719 104709 SRX2635094 SRS2043906 SRA544882 GEO Drummond, Nephrology, Massachusetts General Hospital 1 0.91952   0.24724   0.73884   0.63985   126   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   United States 2017-03-12 Adult Adult Kidney Renal System
41907 41907 SRR5337743 SRX2635093 SRS2043905 SRP101756 PRJNA378882 Transcriptome of the distal late segment of the zebrafish mesonephros GSE96519 Transcriptome Analysis We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.   pubmed:28656378   YS1 GSM2534766   tissue:DL segments|transgene:Tgslc12a3:mCherry|genotype:mCh+|age:adult YS1 none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts DL segments   DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.   transgene:Tgslc12a3:mCherry|genotype:mCh+|age:adult GSM2534766 GSM2534766: YS1; Danio rerio; RNA Seq GSM2534766   1 DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN. GEO Accession:GSM2534766 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP101756     20150717.A-YS1_R1.fastq.gz fastq 7000703892.0 55561142.0 GSM2534766 r1 0:126 A:1521231890;C:1760818628;G:2148863730;T:1569634203;N:155441 126       1521231890 1760818628 2148863730 1569634203 155441 SRX2635093 SRS2043905 SRA544882 GEO Drummond, Nephrology, Massachusetts General Hospital 1 0.96016   0.1982   0.86261   0.75572   126   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   United States 2017-03-12 Adult Adult Kidney Renal System
42599 42599 SRR5810682 SRX2989237 SRS2341160 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of multiple samples 2 GSM2696104   source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes inDrop sequencing of multiple samples 2 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes GSM2696104 GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq GSM2696104   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696104 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     inDrop_v3_run2_R1.fastq.gz fastq 23315853588.0 382227108.0 GSM2696104 r1 0:61 1:0 A:6573828142;C:5137891481;G:5021324431;T:6582457296;N:352238 61 0     6573828142 5137891481 5021324431 6582457296 352238 SRX2989237 SRS2341160 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.83828   0.08537   0.83552   0.56658   61   B   usable mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42600 42600 SRR5810683 SRX2989237 SRS2341160 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of multiple samples 2 GSM2696104   source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes inDrop sequencing of multiple samples 2 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes GSM2696104 GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq GSM2696104   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696104 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     inDrop_v3_run2_R2.fastq.gz fastq 3057816864.0 382227108.0 GSM2696104 r2 0:0 1:8 A:743619897;C:720488231;G:1031094190;T:562297818;N:316728 0 8     743619897 720488231 1031094190 562297818 316728 SRX2989237 SRS2341160 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.0   0.0   1.0       8   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42601 42601 SRR5810684 SRX2989237 SRS2341160 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of multiple samples 2 GSM2696104   source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes inDrop sequencing of multiple samples 2 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes GSM2696104 GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq GSM2696104   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696104 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     inDrop_v3_run2_R3.fastq.gz fastq 3057816864.0 382227108.0 GSM2696104 r3 0:8 A:913664473;C:577895371;G:646194239;T:918893384;N:1169397 8       913664473 577895371 646194239 918893384 1169397 SRX2989237 SRS2341160 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.0   0.0   1.0       8   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42602 42602 SRR5810685 SRX2989237 SRS2341160 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of multiple samples 2 GSM2696104   source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes inDrop sequencing of multiple samples 2 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes GSM2696104 GSM2696104: inDrop sequencing of multiple samples 2; Danio rerio; RNA Seq GSM2696104   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696104 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     inDrop_v3_run2_R4.fastq.gz fastq 5351179512.0 382227108.0 GSM2696104 r4 0:14 A:1351470715;C:1294400719;G:1379073889;T:1322397488;N:3836701 14       1351470715 1294400719 1379073889 1322397488 3836701 SRX2989237 SRS2341160 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.0   0.0   1.0       14   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42603 42603 SRR5810678 SRX2989236 SRS2341159 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of multiple samples 1 GSM2696103   source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes inDrop sequencing of multiple samples 1 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes GSM2696103 GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq GSM2696103   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696103 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     inDrop_v3_run1_R1.fastq.gz fastq 26868371039.0 440465099.0 GSM2696103 r1 0:61 1:0 A:7598044404;C:5948542485;G:5746339343;T:7575168754;N:276053 61 0     7598044404 5948542485 5746339343 7575168754 276053 SRX2989236 SRS2341159 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.83437   0.08222   0.82658   0.54569   61   B   usable mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42604 42604 SRR5810679 SRX2989236 SRS2341159 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of multiple samples 1 GSM2696103   source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes inDrop sequencing of multiple samples 1 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes GSM2696103 GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq GSM2696103   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696103 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     inDrop_v3_run1_R2.fastq.gz fastq 3523720792.0 440465099.0 GSM2696103 r2 0:0 1:8 A:892841722;C:781074758;G:1176856476;T:672376743;N:571093 0 8     892841722 781074758 1176856476 672376743 571093 SRX2989236 SRS2341159 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.0   0.0   1.0       8   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42605 42605 SRR5810680 SRX2989236 SRS2341159 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of multiple samples 1 GSM2696103   source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes inDrop sequencing of multiple samples 1 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes GSM2696103 GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq GSM2696103   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696103 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     inDrop_v3_run1_R3.fastq.gz fastq 3523720792.0 440465099.0 GSM2696103 r3 0:8 A:1016854893;C:682256486;G:759860179;T:1063129659;N:1619575 8       1016854893 682256486 759860179 1063129659 1619575 SRX2989236 SRS2341159 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.0   0.0   1.0       8   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42606 42606 SRR5810681 SRX2989236 SRS2341159 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of multiple samples 1 GSM2696103   source name:Whole kidney marrow|indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes inDrop sequencing of multiple samples 1 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V3 protocol|tissue:kidney marrow|genotype:multiple genotypes GSM2696103 GSM2696103: inDrop sequencing of multiple samples 1; Danio rerio; RNA Seq GSM2696103   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696103 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     inDrop_v3_run1_R4.fastq.gz fastq 6166511386.0 440465099.0 GSM2696103 r4 0:14 A:1513770161;C:1469643118;G:1669791951;T:1509862301;N:3443855 14       1513770161 1469643118 1669791951 1509862301 3443855 SRX2989236 SRS2341159 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.0   0.0   1.0       14   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42607 42607 SRR5810676 SRX2989235 SRS2341158 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2 GSM2696102   source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs GSM2696102 GSM2696102: inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2; Danio rerio; RNA Seq GSM2696102   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696102 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     PRKDC2_R1.fastq.gz fastq 1987929396.0 55220261.0 GSM2696102 r1 0:36 1:0 A:506372087;C:413396954;G:415448050;T:652683387;N:28918 36 0     506372087 413396954 415448050 652683387 28918 SRX2989235 SRS2341158 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.86587   0.12447   0.80336   0.54126   36   B   usable mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42608 42608 SRR5810677 SRX2989235 SRS2341158 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2 GSM2696102   source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs GSM2696102 GSM2696102: inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #2; Danio rerio; RNA Seq GSM2696102   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696102 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     PRKDC2_R2.fastq.gz fastq 2761013050.0 55220261.0 GSM2696102 r2 0:0 1:50 A:554483675;C:506568509;G:721419849;T:974751566;N:3789451 0 50     554483675 506568509 721419849 974751566 3789451 SRX2989235 SRS2341158 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.00796   0.0077   0.99961   0.78947   50   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42609 42609 SRR5810674 SRX2989234 SRS2341157 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1 GSM2696101   source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs GSM2696101 GSM2696101: inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1; Danio rerio; RNA Seq GSM2696101   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696101 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     PRKDC1_R1.fastq.gz fastq 1549442736.0 43040076.0 GSM2696101 r1 0:36 1:0 A:402261661;C:326108405;G:319637981;T:501413963;N:20726 36 0     402261661 326108405 319637981 501413963 20726 SRX2989234 SRS2341157 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.84263   0.11449   0.79464   0.57001   36   B   usable mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42610 42610 SRR5810675 SRX2989234 SRS2341157 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1 GSM2696101   source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:prkdcD3612fs GSM2696101 GSM2696101: inDrop sequencing of prkdcD3612fs homozygous mutant zebrafish sample animal #1; Danio rerio; RNA Seq GSM2696101   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696101 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     PRKDC1_R2.fastq.gz fastq 2152003800.0 43040076.0 GSM2696101 r2 0:0 1:50 A:432547886;C:403759182;G:561234660;T:751564536;N:2897536 0 50     432547886 403759182 561234660 751564536 2897536 SRX2989234 SRS2341157 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.00796   0.00773   0.99971   0.82758   50   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42611 42611 SRR5810672 SRX2989233 SRS2341156 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of WT sample animal #2 GSM2696100   source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype inDrop sequencing of WT sample animal #2 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype GSM2696100 GSM2696100: inDrop sequencing of WT sample animal #2; Danio rerio; RNA Seq GSM2696100   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696100 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     WT2_R1.fastq.gz fastq 3202042500.0 88945625.0 GSM2696100 r1 0:36 1:0 A:821476951;C:657776656;G:665293293;T:1057448635;N:46965 36 0     821476951 657776656 665293293 1057448635 46965 SRX2989233 SRS2341156 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.84222   0.12969   0.80683   0.53542   36   B   usable mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42612 42612 SRR5810673 SRX2989233 SRS2341156 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of WT sample animal #2 GSM2696100   source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype inDrop sequencing of WT sample animal #2 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype GSM2696100 GSM2696100: inDrop sequencing of WT sample animal #2; Danio rerio; RNA Seq GSM2696100   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696100 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     WT2_R2.fastq.gz fastq 4447281250.0 88945625.0 GSM2696100 r2 0:0 1:50 A:880464480;C:827380868;G:1171423978;T:1561925150;N:6086774 0 50     880464480 827380868 1171423978 1561925150 6086774 SRX2989233 SRS2341156 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.00782   0.0075   0.99947   0.91666   50   T   under 1.2% mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System
42613 42613 SRR5810670 SRX2989232 SRS2341155 SRP111339 PRJNA393429 Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] GSE100910 Transcriptome Analysis Recent advances in single cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here we utilized massively parallel single cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs il2rgaY91fs and double homozygous mutant fish identifying blood cell losses in T B and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells classically defined and erythroid primed hematopoietic stem and progenitor cells mucin secreting kidney cells and kidney stem/progenitor cells. In total our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish. Overall design: The goal of our study is to establish the transcriptional profiles of hematopoietic and kidney cell lineages residing in the zebrafish whole kidney marrow. Firstly we performed single cell RNA sequencing by a modified Smart seq2 protocol on sorted single cells from fluorescent transgenic zebrafish lines which label distinct blood cell types n = 246 cells total. Secondly we utilized droplet based single cell RNA sequencing inDrop to investigate unmarked comprehensive hematopoietic lineage structure within wild type casper strain zebrafish N=3 animals n=3 782 cells total. From this we identified ten distinct hematopoietic groups of blood and immune identities. Thirdly we confirmed blood lineage interpretations by comparing hematopoietic lineages within wild type fish with mutant zebrafish with known immunodeficiencies including prkdcD3612fs N=3 animals n=3 201 cells il2rgaY91fs N=2 animals … parent bioproject:PRJNA393415 pubmed:28878000   inDrop sequencing of WT sample animal #1 GSM2696099   source name:Whole kidney marrow|indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype inDrop sequencing of WT sample animal #1 Reads were processed using the indrops pipelinehttps://github.com/indrops/indrops. Briefly reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie. Please see file "inDrop GEO supplementary.xlsx " available on the series record for information on de multiplexing and barcodes for individual samples and cells. Genome build: GRCz10 Supplementary files format and content: text file with read counts. Whole kidney marrow   RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523.   indrop version:inDrop V2 protocol|tissue:kidney marrow|genotype:wildtype GSM2696099 GSM2696099: inDrop sequencing of WT sample animal #1; Danio rerio; RNA Seq GSM2696099   1 RNA from individual cells were reverse transcribed barcoded and unique transcripts are imprinted with UMI all within the droplet. RNA from 1 500 cells of each animal were pooled and subsequently processed together. cDNA products were pre amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit 75 cycles Illumina on a NextSeq 500 platform Illumina. Zebrafish cells are isolated from the kidney marrow into single cell suspensions and treated with 15% Optiprep Sigma. Single cells are microfluidically sorted into droplets containing reverse transcription and barcoding reagents. This method is outlined in Klein et al. PMID 26000487 and Zilionis et al. PMID 27929523. GEO Accession:GSM2696099 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP111339     WT1_R1.fastq.gz fastq 3313205496.0 92033486.0 GSM2696099 r1 0:36 1:0 A:858288917;C:693848400;G:675650809;T:1085369048;N:48322 36 0     858288917 693848400 675650809 1085369048 48322 SRX2989232 SRS2341155 SRA584587 GEO Pathology, Massachusetts General Hospital 1 0.8771   0.13918   0.81115   0.59004   36   B   usable mapping rate illumina nextseq unknown random_priming unknown sc single_cell_droplet indrops   United States 2017-07-07 Undetermined Adult Kidney Renal System

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