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373 rows where experiment.library_layout = "PAIRED" and tissue_curation = "Blood"

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technology 8

experiment.library_selection 6

devstage_curation 6

devstage_curation_coarse 5

experiment.library_strategy 2

experiment.library_source 2

tissue_curation_coarse 1

tissue_curation 1

  • Blood · 373 ✖

experiment.platform 1

experiment.library_layout 1

  • PAIRED · 373 ✖
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
8092 8092 ERR2402432 ERX2443286 ERS2295360 ERP107516 PRJEB25583 The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151 Other The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform. ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14   Hom MO rep3 Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos SAMEA104693977 DPSQ ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693977|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM12|common name:zebrafish|sample name:CM12|scientific name:Danio rerio                 NextSeq 500 paired end sequencing ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 12 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500   ERP107516 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16 CM12.trimmed.read_1.fastq.gz CM12.trimmed.read_2.fastq.gz fastq fastq 5384061477.0 38388598.0 ena RUN DPSQ 14 03 2018 19:09:09:420 12 0:70.70 1:69.55 A:1490429493;C:1197976503;G:1220014984;T:1475615043;N:25454 70 69     1490429493 1197976503 1220014984 1475615043 25454 ERX2443286 ERS2295360 ERA1246315 European Nucleotide Archive Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom 2 0.92285 0.9206 0.06862 0.0688 0.73983 0.74566 0.4752 0.49125 76 75 B B biological fallback assumption illumina nextseq full_length poly_a unknown bulk unknown unknown   United Kingdom 2018-03-14 Undetermined Embryo Blood Hematopoietic System
8093 8093 ERR2402431 ERX2443285 ERS2295359 ERP107516 PRJEB25583 The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151 Other The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform. ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14   Hom MO rep2 Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos SAMEA104693976 DPSQ ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693976|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM11|common name:zebrafish|sample name:CM11|scientific name:Danio rerio                 NextSeq 500 paired end sequencing ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 11 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500   ERP107516 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16 CM11.trimmed.read_1.fastq.gz CM11.trimmed.read_2.fastq.gz fastq fastq 5472085589.0 38860681.0 ena RUN DPSQ 14 03 2018 19:09:09:420 11 0:70.98 1:69.83 A:1514986213;C:1217661004;G:1240412104;T:1499000816;N:25452 70 69     1514986213 1217661004 1240412104 1499000816 25452 ERX2443285 ERS2295359 ERA1246315 European Nucleotide Archive Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom 2 0.91987 0.91874 0.0693 0.07042 0.74042 0.74629 0.48229 0.49144 76 76 B B biological fallback assumption illumina nextseq full_length poly_a unknown bulk unknown unknown   United Kingdom 2018-03-14 Undetermined Embryo Blood Hematopoietic System
8094 8094 ERR2402430 ERX2443284 ERS2295358 ERP107516 PRJEB25583 The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151 Other The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform. ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14   Hom MO rep1 Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos SAMEA104693975 DPSQ ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693975|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM10|common name:zebrafish|sample name:CM10|scientific name:Danio rerio                 NextSeq 500 paired end sequencing ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 10 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500   ERP107516 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16 CM10.trimmed.read_1.fastq.gz CM10.trimmed.read_2.fastq.gz fastq fastq 6091085806.0 43064771.0 ena RUN DPSQ 14 03 2018 19:09:09:420 10 0:71.33 1:70.11 A:1692450462;C:1348639943;G:1375433963;T:1674532019;N:29419 71 70     1692450462 1348639943 1375433963 1674532019 29419 ERX2443284 ERS2295358 ERA1246315 European Nucleotide Archive Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom 2 0.92184 0.92064 0.0699 0.0704 0.74286 0.74874 0.48978 0.48997 75 73 B B biological fallback assumption illumina nextseq full_length poly_a unknown bulk unknown unknown   United Kingdom 2018-03-14 Undetermined Embryo Blood Hematopoietic System
8095 8095 ERR2402429 ERX2443283 ERS2295357 ERP107516 PRJEB25583 The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151 Other The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform. ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14   Hom uninj rep3 Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos SAMEA104693974 DPSQ ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693974|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM9|common name:zebrafish|sample name:CM9|scientific name:Danio rerio                 NextSeq 500 paired end sequencing ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 9 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500   ERP107516 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16 CM9.trimmed.read_1.fastq.gz CM9.trimmed.read_2.fastq.gz fastq fastq 6329252570.0 45070159.0 ena RUN DPSQ 14 03 2018 19:09:09:420 9 0:70.79 1:69.64 A:1753489708;C:1407193617;G:1433449502;T:1735090181;N:29562 70 69     1753489708 1407193617 1433449502 1735090181 29562 ERX2443283 ERS2295357 ERA1246315 European Nucleotide Archive Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom 2 0.91683 0.91616 0.06775 0.06825 0.75158 0.75737 0.49386 0.49199 76 75 B B biological fallback assumption illumina nextseq full_length poly_a unknown bulk unknown unknown   United Kingdom 2018-03-14 Undetermined Embryo Blood Hematopoietic System
8096 8096 ERR2402428 ERX2443282 ERS2295356 ERP107516 PRJEB25583 The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151 Other The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform. ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14   Hom uninj rep2 Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos SAMEA104693973 DPSQ ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693973|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM8|common name:zebrafish|sample name:CM8|scientific name:Danio rerio                 NextSeq 500 paired end sequencing ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 8 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500   ERP107516 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16 CM8.trimmed.read_1.fastq.gz CM8.trimmed.read_2.fastq.gz fastq fastq 5405185494.0 38637007.0 ena RUN DPSQ 14 03 2018 19:09:09:420 8 0:70.45 1:69.44 A:1491577735;C:1206599147;G:1229354248;T:1477628006;N:26358 70 69     1491577735 1206599147 1229354248 1477628006 26358 ERX2443282 ERS2295356 ERA1246315 European Nucleotide Archive Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom 2 0.91776 0.91567 0.07134 0.07241 0.7517 0.75716 0.47952 0.48745 73 73 B B biological fallback assumption illumina nextseq full_length poly_a unknown bulk unknown unknown   United Kingdom 2018-03-14 Undetermined Embryo Blood Hematopoietic System
8097 8097 ERR2402427 ERX2443281 ERS2295355 ERP107516 PRJEB25583 The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151 Other The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform. ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14   Hom uninj rep1 Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos SAMEA104693972 DPSQ ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693972|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM7|common name:zebrafish|sample name:CM7|scientific name:Danio rerio                 NextSeq 500 paired end sequencing ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 7 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500   ERP107516 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16 CM7.trimmed.read_1.fastq.gz CM7.trimmed.read_2.fastq.gz fastq fastq 6262947202.0 44863127.0 ena RUN DPSQ 14 03 2018 19:09:09:420 7 0:70.28 1:69.32 A:1732018658;C:1394742098;G:1420957611;T:1715198292;N:30543 70 69     1732018658 1394742098 1420957611 1715198292 30543 ERX2443281 ERS2295355 ERA1246315 European Nucleotide Archive Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom 2 0.91622 0.9144 0.0754 0.07588 0.74886 0.75371 0.48672 0.48471 76 76 B B biological fallback assumption illumina nextseq full_length poly_a unknown bulk unknown unknown   United Kingdom 2018-03-14 Undetermined Embryo Blood Hematopoietic System
8098 8098 ERR2402426 ERX2443280 ERS2295354 ERP107516 PRJEB25583 The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151 Other The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform. ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14   Het MO rep3 Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos SAMEA104693971 DPSQ ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693971|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM6|common name:zebrafish|sample name:CM6|scientific name:Danio rerio                 NextSeq 500 paired end sequencing ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 6 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500   ERP107516 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16 CM6.trimmed.read_1.fastq.gz CM6.trimmed.read_2.fastq.gz fastq fastq 5819615834.0 41591499.0 ena RUN DPSQ 14 03 2018 19:09:09:420 6 0:70.47 1:69.45 A:1594833553;C:1309877713;G:1335153588;T:1579722744;N:28236 70 69     1594833553 1309877713 1335153588 1579722744 28236 ERX2443280 ERS2295354 ERA1246315 European Nucleotide Archive Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom 2 0.92 0.9183 0.0573 0.05793 0.77362 0.778 0.47792 0.46987 76 75 B B biological fallback assumption illumina nextseq full_length poly_a unknown bulk unknown unknown   United Kingdom 2018-03-14 Undetermined Embryo Blood Hematopoietic System
8099 8099 ERR2402425 ERX2443279 ERS2295353 ERP107516 PRJEB25583 The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151 Other The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform. ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14   Het MO rep2 Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos SAMEA104693970 DPSQ ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693970|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM5|common name:zebrafish|sample name:CM5|scientific name:Danio rerio                 NextSeq 500 paired end sequencing ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 5 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500   ERP107516 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16 CM5.trimmed.read_1.fastq.gz CM5.trimmed.read_2.fastq.gz fastq fastq 5573895202.0 39518227.0 ena RUN DPSQ 14 03 2018 19:09:09:420 5 0:71.02 1:70.03 A:1530297250;C:1251775796;G:1276506882;T:1515288256;N:27018 71 70     1530297250 1251775796 1276506882 1515288256 27018 ERX2443279 ERS2295353 ERA1246315 European Nucleotide Archive Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom 2 0.92217 0.92081 0.06807 0.06843 0.76926 0.77441 0.45543 0.48098 76 75 B B biological fallback assumption illumina nextseq full_length poly_a unknown bulk unknown unknown   United Kingdom 2018-03-14 Undetermined Embryo Blood Hematopoietic System
8100 8100 ERR2402424 ERX2443278 ERS2295352 ERP107516 PRJEB25583 The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151 Other The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform. ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14   Het MO rep1 Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos SAMEA104693969 DPSQ ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693969|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM4|common name:zebrafish|sample name:CM4|scientific name:Danio rerio                 NextSeq 500 paired end sequencing ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 4 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500   ERP107516 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16 CM4.trimmed.read_1.fastq.gz CM4.trimmed.read_2.fastq.gz fastq fastq 5803404091.0 41335851.0 ena RUN DPSQ 14 03 2018 19:09:09:420 4 0:70.72 1:69.67 A:1590577583;C:1305683925;G:1331895549;T:1575219146;N:27888 70 69     1590577583 1305683925 1331895549 1575219146 27888 ERX2443278 ERS2295352 ERA1246315 European Nucleotide Archive Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom 2 0.9216 0.91971 0.05719 0.05738 0.77333 0.77761 0.47789 0.47244 76 74 B B biological fallback assumption illumina nextseq full_length poly_a unknown bulk unknown unknown   United Kingdom 2018-03-14 Undetermined Embryo Blood Hematopoietic System
8101 8101 ERR2402423 ERX2443277 ERS2295351 ERP107516 PRJEB25583 The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151 Other The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform. ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14   Het uninj rep3 Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos SAMEA104693968 DPSQ ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693968|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM3|common name:zebrafish|sample name:CM3|scientific name:Danio rerio                 NextSeq 500 paired end sequencing ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 3 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500   ERP107516 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16 CM3.trimmed.read_1.fastq.gz CM3.trimmed.read_2.fastq.gz fastq fastq 5992797058.0 42390223.0 ena RUN DPSQ 14 03 2018 19:09:09:420 3 0:71.26 1:70.11 A:1639390320;C:1352082344;G:1378624207;T:1622672043;N:28144 71 70     1639390320 1352082344 1378624207 1622672043 28144 ERX2443277 ERS2295351 ERA1246315 European Nucleotide Archive Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom 2 0.92104 0.92006 0.07044 0.07056 0.77506 0.78137 0.48154 0.46497 75 75 B B biological fallback assumption illumina nextseq full_length poly_a unknown bulk unknown unknown   United Kingdom 2018-03-14 Undetermined Embryo Blood Hematopoietic System
8102 8102 ERR2402422 ERX2443276 ERS2295350 ERP107516 PRJEB25583 The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151 Other The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform. ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14   Het uninj rep2 Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos SAMEA104693967 DPSQ ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693967|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM2|common name:zebrafish|sample name:CM2|scientific name:Danio rerio                 NextSeq 500 paired end sequencing ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500   ERP107516 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16 CM2.trimmed.read_2.fastq.gz CM2.trimmed.read_1.fastq.gz fastq fastq 5611396868.0 39759688.0 ena RUN DPSQ 14 03 2018 19:09:09:420 2 0:71.11 1:70.02 A:1537234166;C:1262883447;G:1288444384;T:1522807333;N:27538 71 70     1537234166 1262883447 1288444384 1522807333 27538 ERX2443276 ERS2295350 ERA1246315 European Nucleotide Archive Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom 2 0.91881 0.91733 0.06861 0.06958 0.77238 0.77883 0.48415 0.47367 76 73 B B biological fallback assumption illumina nextseq full_length poly_a unknown bulk unknown unknown   United Kingdom 2018-03-14 Undetermined Embryo Blood Hematopoietic System
8103 8103 ERR2402421 ERX2443275 ERS2295349 ERP107516 PRJEB25583 The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151 Other The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform. ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14   Het uninj rep1 Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos SAMEA104693966 DPSQ ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693966|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM1|common name:zebrafish|sample name:CM1|scientific name:Danio rerio                 NextSeq 500 paired end sequencing ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500   ERP107516 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16 CM1.trimmed.read_1.fastq.gz CM1.trimmed.read_2.fastq.gz fastq fastq 6229432533.0 44233290.0 ena RUN DPSQ 14 03 2018 19:09:09:420 1 0:70.98 1:69.85 A:1712806281;C:1395764700;G:1423415860;T:1697416127;N:29565 70 69     1712806281 1395764700 1423415860 1697416127 29565 ERX2443275 ERS2295349 ERA1246315 European Nucleotide Archive Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom 2 0.91818 0.9169 0.07104 0.07095 0.77585 0.78066 0.47896 0.46653 56 56 B B biological fallback assumption illumina nextseq full_length poly_a unknown bulk unknown unknown   United Kingdom 2018-03-14 Undetermined Embryo Blood Hematopoietic System
24784 24784 SRR25502048 SRX21232930 SRS18488024 SRP453114 PRJNA1001808 The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger GSE239949 Transcriptome Analysis From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.   pubmed:28382966   Sample 15 05316 MCK mut3 GSM7678168   tissue:lyz+ mpx+ granulocytes|cell type:lyz+ mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf|geo loc name:missing|collection date:missing Sample 15 05316 MCK mut3 Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample lyz+ mpx+ granulocytes   RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.   cell type:lyz+ mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf GSM7678168 GSM7678168: Sample 15 05316 MCK mut3; Danio rerio; RNA Seq GSM7678168 r1 GSM7678168 1 RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP453114     15-05316_MCK_mut3_GTGCTT_L002_R1_001.fastq.gz 15-05316_MCK_mut3_GTGCTT_L002_R2_001.fastq.gz fastq fastq 4329868620.0 20618422.0 GSM7678168 r1 0:105 1:105 A:1075032412;C:1077085067;G:1119735718;T:1057797736;N:217687 105 105     1075032412 1077085067 1119735718 1057797736 217687 SRX21232930 SRS18488024 SRA1685493 Rural Clinical Sciences, La Trobe University Rural Clinical Sciences, La Trobe University 2 0.78961 0.91048 0.20166 0.23232 0.81556 0.81115 0.59478 0.59379 105 105 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-08-03 Hatching Embryo Blood Hematopoietic System
24785 24785 SRR25502049 SRX21232929 SRS18488023 SRP453114 PRJNA1001808 The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger GSE239949 Transcriptome Analysis From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.   pubmed:28382966   Sample 15 05316 MCK mut2 GSM7678167   tissue:lyz+ mpx+ granulocytes|cell type:lyz+ mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf|geo loc name:missing|collection date:missing Sample 15 05316 MCK mut2 Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample lyz+ mpx+ granulocytes   RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.   cell type:lyz+ mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf GSM7678167 GSM7678167: Sample 15 05316 MCK mut2; Danio rerio; RNA Seq GSM7678167 r1 GSM7678167 1 RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP453114     15-05316_MCK_mut2_ACCTCA_L002_R1_001.fastq.gz 15-05316_MCK_mut2_ACCTCA_L002_R2_001.fastq.gz fastq fastq 4444374270.0 21163687.0 GSM7678167 r1 0:105 1:105 A:1114919906;C:1098541058;G:1145427151;T:1085262902;N:223253 105 105     1114919906 1098541058 1145427151 1085262902 223253 SRX21232929 SRS18488023 SRA1685493 Rural Clinical Sciences, La Trobe University Rural Clinical Sciences, La Trobe University 2 0.74961 0.90068 0.18596 0.22057 0.81115 0.80754 0.5829 0.58615 105 105 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-08-03 Hatching Embryo Blood Hematopoietic System
24786 24786 SRR25502050 SRX21232928 SRS18488022 SRP453114 PRJNA1001808 The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger GSE239949 Transcriptome Analysis From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.   pubmed:28382966   Sample 15 05316 MCK mut1 GSM7678166   tissue:lyz+ mpx+ granulocytes|cell type:lyz+ mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf|geo loc name:missing|collection date:missing Sample 15 05316 MCK mut1 Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample lyz+ mpx+ granulocytes   RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.   cell type:lyz+ mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf GSM7678166 GSM7678166: Sample 15 05316 MCK mut1; Danio rerio; RNA Seq GSM7678166 r1 GSM7678166 1 RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP453114     15-05316_MCK_mut1_GCACTA_L002_R1_001.fastq.gz 15-05316_MCK_mut1_GCACTA_L002_R2_001.fastq.gz fastq fastq 4459467180.0 21235558.0 GSM7678166 r1 0:105 1:105 A:1206908747;C:1012207561;G:1060393698;T:1179731376;N:225798 105 105     1206908747 1012207561 1060393698 1179731376 225798 SRX21232928 SRS18488022 SRA1685493 Rural Clinical Sciences, La Trobe University Rural Clinical Sciences, La Trobe University 2 0.75719 0.88462 0.20719 0.24095 0.78559 0.77914 0.50538 0.55691 105 105 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-08-03 Hatching Embryo Blood Hematopoietic System
24787 24787 SRR25502051 SRX21232927 SRS18488021 SRP453114 PRJNA1001808 The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger GSE239949 Transcriptome Analysis From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.   pubmed:28382966   Sample 15 05315 MCK WT3 GSM7678165   tissue:lyz+ mpx+ granulocytes|cell type:lyz+ mpx+ granulocytes|genotype:wild type|age:48 hpf|geo loc name:missing|collection date:missing Sample 15 05315 MCK WT3 Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample lyz+ mpx+ granulocytes   RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.   cell type:lyz+ mpx+ granulocytes|genotype:wild type|age:48 hpf GSM7678165 GSM7678165: Sample 15 05315 MCK WT3; Danio rerio; RNA Seq GSM7678165 r1 GSM7678165 1 RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP453114     15-05315_MCK_WT3_AGTGAG_L002_R1_001.fastq.gz 15-05315_MCK_WT3_AGTGAG_L002_R2_001.fastq.gz fastq fastq 3925329240.0 18692044.0 GSM7678165 r1 0:105 1:105 A:1022654212;C:930239389;G:973328942;T:998905803;N:200894 105 105     1022654212 930239389 973328942 998905803 200894 SRX21232927 SRS18488021 SRA1685493 Rural Clinical Sciences, La Trobe University Rural Clinical Sciences, La Trobe University 2 0.75647 0.89377 0.19165 0.22718 0.81057 0.80501 0.51173 0.54819 105 105 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-08-03 Hatching Embryo Blood Hematopoietic System
24788 24788 SRR25502052 SRX21232926 SRS18488020 SRP453114 PRJNA1001808 The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger GSE239949 Transcriptome Analysis From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.   pubmed:28382966   Sample 15 05314 MCK WT2 GSM7678164   tissue:lyz+ mpx+ granulocytes|cell type:lyz+ mpx+ granulocytes|genotype:wild type|age:48 hpf|geo loc name:missing|collection date:missing Sample 15 05314 MCK WT2 Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample lyz+ mpx+ granulocytes   RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.   cell type:lyz+ mpx+ granulocytes|genotype:wild type|age:48 hpf GSM7678164 GSM7678164: Sample 15 05314 MCK WT2; Danio rerio; RNA Seq GSM7678164 r1 GSM7678164 1 RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP453114     15-05314_MCK_WT2_TGGTGA_L002_R2_001.fastq.gz 15-05314_MCK_WT2_TGGTGA_L002_R1_001.fastq.gz fastq fastq 4100489820.0 19526142.0 GSM7678164 r1 0:105 1:105 A:1022482319;C:1016090490;G:1063619365;T:998086417;N:211229 105 105     1022482319 1016090490 1063619365 998086417 211229 SRX21232926 SRS18488020 SRA1685493 Rural Clinical Sciences, La Trobe University Rural Clinical Sciences, La Trobe University 2 0.76378 0.90522 0.20093 0.23619 0.82467 0.82049 0.57261 0.562 105 105 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-08-03 Hatching Embryo Blood Hematopoietic System
24789 24789 SRR25502053 SRX21232925 SRS18488019 SRP453114 PRJNA1001808 The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger GSE239949 Transcriptome Analysis From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.   pubmed:28382966   Sample 15 05313 MCK WT1 GSM7678163   tissue:lyz+ mpx+ granulocytes|cell type:lyz+ mpx+ granulocytes|genotype:wild type|age:48 hpf|geo loc name:missing|collection date:missing Sample 15 05313 MCK WT1 Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample lyz+ mpx+ granulocytes   RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.   cell type:lyz+ mpx+ granulocytes|genotype:wild type|age:48 hpf GSM7678163 GSM7678163: Sample 15 05313 MCK WT1; Danio rerio; RNA Seq GSM7678163 r1 GSM7678163 1 RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 1500   SRP453114     15-05313_MCK_WT1_AACCAG_L002_R1_001.fastq.gz 15-05313_MCK_WT1_AACCAG_L002_R2_001.fastq.gz fastq fastq 4135721100.0 19693910.0 GSM7678163 r1 0:105 1:105 A:1048700719;C:1014162128;G:1070155053;T:1002495763;N:207437 105 105     1048700719 1014162128 1070155053 1002495763 207437 SRX21232925 SRS18488019 SRA1685493 Rural Clinical Sciences, La Trobe University Rural Clinical Sciences, La Trobe University 2 0.70974 0.9073 0.1771 0.22534 0.82483 0.81625 0.56311 0.55183 105 105 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Australia 2023-08-03 Hatching Embryo Blood Hematopoietic System
25302 25302 SRR25793493 SRX21515745 SRS18742910 SRP457465 PRJNA1010662 The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis. PRJNA1010662 Other Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.       Single cell Pr1phros ADULT miR 144 mutant Danio rerio miR 144   isolate:miR 144 mutant|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:blood|BioSampleModel:Model organism or animal                 Single cell Pr1phros ADULT miR 144 mutant Danio rerio CD 144 1 CD 144 1 Single cell library cloning was done with 10X Genomics     RNA-Seq TRANSCRIPTOMIC SINGLE CELL unspecified PAIRED ILLUMINA NextSeq 2000   SRP457465     CD_144_1_S3_R1.fastq CD_144_1_S3_R2.fastq fastq fastq 12899093774.0 108395746.0 CD 144 1 S3 R1.fastq 0:28 1:91 A:3225260764;C:3211986177;G:3151471558;T:3308055659;N:2319616 28 91     3225260764 3211986177 3151471558 3308055659 2319616 SRX21515745 SRS18742910 SRA1701829 University of East Anglia|Biological Sciences University of East Anglia 2 0.00483 0.97382 0.00157 0.05913 0.99439 0.86815 0.46634 0.45907 28 91 T B sc-like readlen illumina nextseq_v2 unknown unknown unknown sc single_cell_droplet 10x   United Kingdom 2023-08-30 Adult Adult Blood Hematopoietic System
25303 25303 SRR25793494 SRX21515744 SRS18742909 SRP457465 PRJNA1010662 The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis. PRJNA1010662 Other Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.       Single cell Pr1phros ADULT Wild type Danio rerio WT   isolate:Wildtype|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:blood|BioSampleModel:Model organism or animal                 Single cell Pr1phros ADULT Wild type Danio rerio CD wt 1 CD wt 1 Single cell library cloning was done with 10X Genomics     RNA-Seq TRANSCRIPTOMIC SINGLE CELL unspecified PAIRED ILLUMINA NextSeq 2000   SRP457465     CD_wt_1_S2_R1.fastq CD_wt_1_S2_R2.fastq fastq fastq 12715533299.0 106853221.0 CD wt 1 S2 R1.fastq 0:28 1:91 A:3324705878;C:3042843364;G:3105568183;T:3240105528;N:2310346 28 91     3324705878 3042843364 3105568183 3240105528 2310346 SRX21515744 SRS18742909 SRA1701829 University of East Anglia|Biological Sciences University of East Anglia 2 0.00593 0.93177 0.00191 0.09596 0.99257 0.84394 0.42447 0.4869 28 91 T B sc-like readlen illumina nextseq_v2 unknown unknown unknown sc single_cell_droplet 10x   United Kingdom 2023-08-30 Adult Adult Blood Hematopoietic System
28902 28902 SRR26827532 SRX22524052 SRS19535497 SRP471831 PRJNA1040223 The Caudal Hematopoietic Tissue is Differentially Required for Erythrocytes and Neutrophils from Definitive Hematopoiesis in Zebrafish GSE247730 Transcriptome Analysis Neutrophils and erythrocytes are vital to the immune system and oxygen transport respectively. However the mechanisms by which hematopoietic niches support their development remain incompletely understood. In hematopoiesis research zebrafish larvae are a common model for studying the development of definitive neutrophils and erythrocytes in the caudal hematopoietic tissue. In this study we showed that erythrocytes predominantly reside inside the blood vessels of the CHT while neutrophils stay outside. Ectopic vascular endothelium induced by Bone Morphogenetic Protein 2bBmp2b overexpression attracts both cell types with erythrocytes inside and neutrophils outside. CHT removal has minimal impact on definitive neutrophils from the ventral wall of the dorsal aorta VDA but severely affects definitive erythrocytes from the same source. Bulk RNA sequencing identified epoa as a vital factor for erythrocyte generation within CHT endothelium. Overexpression of epoa through the lyve1b promoter which is specifically expressed in vein lymphatic vessels and CHT vein endothelial cells rescued the erythrocyte reduction in epoa mutants. Our study reveals that the caudal hematopoietic tissue is differentially required for definitive erythrocytes and neutrophils. Overall design: We then performed gene expression profiling analysis using data obtained from BULK RNA seq of 5dpf vein endothelium cells and endothelium cells.       vein endothelium cells Day5 rep2 GSM7899809   source name:Caudal hematopoietic tissue|tissue:Caudal hematopoietic tissue|cell type:vein endothelium cells|genotype:Wildtype|treatment:no treatment|geo loc name:missing|collection date:missing vein endothelium cells Day5 rep2 Filtering of Clean Reads by fastp version 0.18.0.The parameters were as follows:1 removing reads containing adapters; 2 removing reads containing more than 10% of unknown nucleotides N; 3 removing low quality reads containing more than 50% of low quality Q value≤20 bases. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. An index of the reference genome was built and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 with “ rna strandness RF” and other parameters set as a default.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments Principal component analysis PCA was performed with R package gmodels http://www.r project.org/ in this experience;RNAs differential expression analysis was performed by DESeq2; Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample Caudal hematopoietic tissue   Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.   tissue:Caudal hematopoietic tissue|cell type:vein endothelium cells|genotype:Wildtype|treatment:no treatment GSM7899809 GSM7899809: vein endothelium cells Day5 rep2; Danio rerio; RNA Seq GSM7899809 r1 GSM7899809 1 Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471831   loader:fastq load.py vein_endothelium_cells-2_1.fq.gz vein_endothelium_cells-2_2.fq.gz fastq fastq 9110989800.0 30369966.0 GSM7899809 r1 0:150 1:150 A:2454542720;C:2090617752;G:2126374129;T:2439172440;N:282759 150 150     2454542720 2090617752 2126374129 2439172440 282759 SRX22524052 SRS19535497 SRA1750986 South China University of Technology South China University of Technology 2 0.89413 0.89048 0.1507 0.14922 0.78466 0.78496 0.5263 0.5335 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk bulk bulk   China 2023-11-14 Larval Larval Blood Hematopoietic System
28903 28903 SRR26827533 SRX22524051 SRS19535496 SRP471831 PRJNA1040223 The Caudal Hematopoietic Tissue is Differentially Required for Erythrocytes and Neutrophils from Definitive Hematopoiesis in Zebrafish GSE247730 Transcriptome Analysis Neutrophils and erythrocytes are vital to the immune system and oxygen transport respectively. However the mechanisms by which hematopoietic niches support their development remain incompletely understood. In hematopoiesis research zebrafish larvae are a common model for studying the development of definitive neutrophils and erythrocytes in the caudal hematopoietic tissue. In this study we showed that erythrocytes predominantly reside inside the blood vessels of the CHT while neutrophils stay outside. Ectopic vascular endothelium induced by Bone Morphogenetic Protein 2bBmp2b overexpression attracts both cell types with erythrocytes inside and neutrophils outside. CHT removal has minimal impact on definitive neutrophils from the ventral wall of the dorsal aorta VDA but severely affects definitive erythrocytes from the same source. Bulk RNA sequencing identified epoa as a vital factor for erythrocyte generation within CHT endothelium. Overexpression of epoa through the lyve1b promoter which is specifically expressed in vein lymphatic vessels and CHT vein endothelial cells rescued the erythrocyte reduction in epoa mutants. Our study reveals that the caudal hematopoietic tissue is differentially required for definitive erythrocytes and neutrophils. Overall design: We then performed gene expression profiling analysis using data obtained from BULK RNA seq of 5dpf vein endothelium cells and endothelium cells.       vein endothelium cells Day5 rep1 GSM7899808   source name:Caudal hematopoietic tissue|tissue:Caudal hematopoietic tissue|cell type:vein endothelium cells|genotype:Wildtype|treatment:no treatment|geo loc name:missing|collection date:missing vein endothelium cells Day5 rep1 Filtering of Clean Reads by fastp version 0.18.0.The parameters were as follows:1 removing reads containing adapters; 2 removing reads containing more than 10% of unknown nucleotides N; 3 removing low quality reads containing more than 50% of low quality Q value≤20 bases. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. An index of the reference genome was built and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 with “ rna strandness RF” and other parameters set as a default.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments Principal component analysis PCA was performed with R package gmodels http://www.r project.org/ in this experience;RNAs differential expression analysis was performed by DESeq2; Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample Caudal hematopoietic tissue   Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.   tissue:Caudal hematopoietic tissue|cell type:vein endothelium cells|genotype:Wildtype|treatment:no treatment GSM7899808 GSM7899808: vein endothelium cells Day5 rep1; Danio rerio; RNA Seq GSM7899808 r1 GSM7899808 1 Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471831   loader:fastq load.py vein_endothelium_cells-1_2.fq.gz vein_endothelium_cells-1_1.fq.gz fastq fastq 8585973300.0 28619911.0 GSM7899808 r1 0:150 1:150 A:2253650188;C:2015841518;G:2037568162;T:2278266858;N:646574 150 150     2253650188 2015841518 2037568162 2278266858 646574 SRX22524051 SRS19535496 SRA1750986 South China University of Technology South China University of Technology 2 0.8876 0.88392 0.14777 0.14719 0.78969 0.79038 0.53142 0.53136 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk bulk bulk   China 2023-11-14 Larval Larval Blood Hematopoietic System
28904 28904 SRR26827534 SRX22524050 SRS19535495 SRP471831 PRJNA1040223 The Caudal Hematopoietic Tissue is Differentially Required for Erythrocytes and Neutrophils from Definitive Hematopoiesis in Zebrafish GSE247730 Transcriptome Analysis Neutrophils and erythrocytes are vital to the immune system and oxygen transport respectively. However the mechanisms by which hematopoietic niches support their development remain incompletely understood. In hematopoiesis research zebrafish larvae are a common model for studying the development of definitive neutrophils and erythrocytes in the caudal hematopoietic tissue. In this study we showed that erythrocytes predominantly reside inside the blood vessels of the CHT while neutrophils stay outside. Ectopic vascular endothelium induced by Bone Morphogenetic Protein 2bBmp2b overexpression attracts both cell types with erythrocytes inside and neutrophils outside. CHT removal has minimal impact on definitive neutrophils from the ventral wall of the dorsal aorta VDA but severely affects definitive erythrocytes from the same source. Bulk RNA sequencing identified epoa as a vital factor for erythrocyte generation within CHT endothelium. Overexpression of epoa through the lyve1b promoter which is specifically expressed in vein lymphatic vessels and CHT vein endothelial cells rescued the erythrocyte reduction in epoa mutants. Our study reveals that the caudal hematopoietic tissue is differentially required for definitive erythrocytes and neutrophils. Overall design: We then performed gene expression profiling analysis using data obtained from BULK RNA seq of 5dpf vein endothelium cells and endothelium cells.       non vein endothelium cells Control Day5 rep2 GSM7899807   source name:Caudal hematopoietic tissue|tissue:Caudal hematopoietic tissue|cell type:non vein endothelium cells|genotype:Wildtype|treatment:no treatment|geo loc name:missing|collection date:missing non vein endothelium cells Control Day5 rep2 Filtering of Clean Reads by fastp version 0.18.0.The parameters were as follows:1 removing reads containing adapters; 2 removing reads containing more than 10% of unknown nucleotides N; 3 removing low quality reads containing more than 50% of low quality Q value≤20 bases. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. An index of the reference genome was built and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 with “ rna strandness RF” and other parameters set as a default.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments Principal component analysis PCA was performed with R package gmodels http://www.r project.org/ in this experience;RNAs differential expression analysis was performed by DESeq2; Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample Caudal hematopoietic tissue   Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.   tissue:Caudal hematopoietic tissue|cell type:non vein endothelium cells|genotype:Wildtype|treatment:no treatment GSM7899807 GSM7899807: non vein endothelium cells Control Day5 rep2; Danio rerio; RNA Seq GSM7899807 r1 GSM7899807 1 Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471831   loader:fastq load.py non-vein_endothelium_cells-2_1.fq.gz non-vein_endothelium_cells-2_2.fq.gz fastq fastq 9363942600.0 31213142.0 GSM7899807 r1 0:150 1:150 A:2523111369;C:2155598161;G:2171776473;T:2513164552;N:292045 150 150     2523111369 2155598161 2171776473 2513164552 292045 SRX22524050 SRS19535495 SRA1750986 South China University of Technology South China University of Technology 2 0.93879 0.93706 0.10971 0.10945 0.76721 0.76737 0.51346 0.51513 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk bulk bulk   China 2023-11-14 Larval Larval Blood Hematopoietic System
28905 28905 SRR26827535 SRX22524049 SRS19535494 SRP471831 PRJNA1040223 The Caudal Hematopoietic Tissue is Differentially Required for Erythrocytes and Neutrophils from Definitive Hematopoiesis in Zebrafish GSE247730 Transcriptome Analysis Neutrophils and erythrocytes are vital to the immune system and oxygen transport respectively. However the mechanisms by which hematopoietic niches support their development remain incompletely understood. In hematopoiesis research zebrafish larvae are a common model for studying the development of definitive neutrophils and erythrocytes in the caudal hematopoietic tissue. In this study we showed that erythrocytes predominantly reside inside the blood vessels of the CHT while neutrophils stay outside. Ectopic vascular endothelium induced by Bone Morphogenetic Protein 2bBmp2b overexpression attracts both cell types with erythrocytes inside and neutrophils outside. CHT removal has minimal impact on definitive neutrophils from the ventral wall of the dorsal aorta VDA but severely affects definitive erythrocytes from the same source. Bulk RNA sequencing identified epoa as a vital factor for erythrocyte generation within CHT endothelium. Overexpression of epoa through the lyve1b promoter which is specifically expressed in vein lymphatic vessels and CHT vein endothelial cells rescued the erythrocyte reduction in epoa mutants. Our study reveals that the caudal hematopoietic tissue is differentially required for definitive erythrocytes and neutrophils. Overall design: We then performed gene expression profiling analysis using data obtained from BULK RNA seq of 5dpf vein endothelium cells and endothelium cells.       non vein endothelium cells Control Day5 rep1 GSM7899806   source name:Caudal hematopoietic tissue|tissue:Caudal hematopoietic tissue|cell type:non vein endothelium cells|genotype:Wildtype|treatment:no treatment|geo loc name:missing|collection date:missing non vein endothelium cells Control Day5 rep1 Filtering of Clean Reads by fastp version 0.18.0.The parameters were as follows:1 removing reads containing adapters; 2 removing reads containing more than 10% of unknown nucleotides N; 3 removing low quality reads containing more than 50% of low quality Q value≤20 bases. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. An index of the reference genome was built and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 with “ rna strandness RF” and other parameters set as a default.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments Principal component analysis PCA was performed with R package gmodels http://www.r project.org/ in this experience;RNAs differential expression analysis was performed by DESeq2; Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample Caudal hematopoietic tissue   Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.   tissue:Caudal hematopoietic tissue|cell type:non vein endothelium cells|genotype:Wildtype|treatment:no treatment GSM7899806 GSM7899806: non vein endothelium cells Control Day5 rep1; Danio rerio; RNA Seq GSM7899806 r1 GSM7899806 1 Non vein endothelium cells and vein endothelium cells were collected from 5dpf of Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP471831   loader:fastq load.py non-vein_endothelium_cells-1_1.fq.gz non-vein_endothelium_cells-1_2.fq.gz fastq fastq 8396176800.0 27987256.0 GSM7899806 r1 0:150 1:150 A:2190594419;C:1990596503;G:2019391921;T:2194713332;N:880625 150 150     2190594419 1990596503 2019391921 2194713332 880625 SRX22524049 SRS19535494 SRA1750986 South China University of Technology South China University of Technology 2 0.94508 0.94385 0.0967 0.09697 0.77642 0.77632 0.49896 0.49962 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk bulk bulk   China 2023-11-14 Larval Larval Blood Hematopoietic System
29175 29175 SRR27292304 SRX22969963 SRS19936063 SRP479046 PRJNA1054617 Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish GSE250610 Transcriptome Analysis Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…   pubmed:38922186   Burned Larval Zebrafish 48 hours post burn GSM7982886   source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing Burned Larval Zebrafish 48 hours post burn FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix Whole blood Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer. Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator. tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn GSM7982886 GSM7982886: Burned Larval Zebrafish 48 hours post burn; Danio rerio; RNA Seq GSM7982886 r1 GSM7982886 1 Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP479046   loader:fastq load.py Burn-48hpb_S5_L001_R2_001.fastq.gz Burn-48hpb_S5_L001_R1_001.fastq.gz fastq fastq 20874980529.0 178418637.0 GSM7982886 r1 0:28 1:89 A:5945091269;C:4392590896;G:4497688824;T:6035946283;N:3663257 28 89     5945091269 4392590896 4497688824 6035946283 3663257 SRX22969963 SRS19936063 SRA1772557 University of Wisconsin-Madison University of Wisconsin-Madison 2 0.00573 0.91666 0.00222 0.19474 0.9931 0.79306 0.42082 0.53801 28 89 T B sc-like readlen illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United States 2023-12-19 Multi-stage Multi-stage Blood Hematopoietic System
29176 29176 SRR27292305 SRX22969963 SRS19936063 SRP479046 PRJNA1054617 Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish GSE250610 Transcriptome Analysis Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…   pubmed:38922186   Burned Larval Zebrafish 48 hours post burn GSM7982886   source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing Burned Larval Zebrafish 48 hours post burn FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix Whole blood Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer. Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator. tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn GSM7982886 GSM7982886: Burned Larval Zebrafish 48 hours post burn; Danio rerio; RNA Seq GSM7982886 r1 GSM7982886 1 Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP479046   loader:fastq load.py Burn-48hpb_S5_L002_R1_001.fastq.gz Burn-48hpb_S5_L002_R2_001.fastq.gz fastq fastq 20022973425.0 171136525.0 GSM7982886 r2 0:28 1:89 A:5709681181;C:4208386174;G:4307510275;T:5796282368;N:1113427 28 89     5709681181 4208386174 4307510275 5796282368 1113427 SRX22969963 SRS19936063 SRA1772557 University of Wisconsin-Madison University of Wisconsin-Madison 2 0.00547 0.9154 0.00202 0.1955 0.99283 0.79423 0.39307 0.53427 28 89 T B sc-like readlen illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United States 2023-12-19 Multi-stage Multi-stage Blood Hematopoietic System
29177 29177 SRR27292306 SRX22969962 SRS19936064 SRP479046 PRJNA1054617 Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish GSE250610 Transcriptome Analysis Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…   pubmed:38922186   Burned Larval Zebrafish 24 hours post burn GSM7982885   source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing Burned Larval Zebrafish 24 hours post burn FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix Whole blood Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer. Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator. tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn GSM7982885 GSM7982885: Burned Larval Zebrafish 24 hours post burn; Danio rerio; RNA Seq GSM7982885 r1 GSM7982885 1 Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP479046   loader:fastq load.py Burn-24hpb_S2_L001_R1_001.fastq.gz Burn-24hpb_S2_L001_R2_001.fastq.gz fastq fastq 9782870058.0 83614274.0 GSM7982885 r1 0:28 1:89 A:2744737668;C:2140848416;G:2249400157;T:2645170677;N:2713140 28 89     2744737668 2140848416 2249400157 2645170677 2713140 SRX22969962 SRS19936064 SRA1772557 University of Wisconsin-Madison University of Wisconsin-Madison 2 0.00752 0.92059 0.00244 0.16143 0.98944 0.82929 0.44176 0.54525 28 89 T B sc-like readlen illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United States 2023-12-19 Multi-stage Multi-stage Blood Hematopoietic System
29178 29178 SRR27292307 SRX22969962 SRS19936064 SRP479046 PRJNA1054617 Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish GSE250610 Transcriptome Analysis Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…   pubmed:38922186   Burned Larval Zebrafish 24 hours post burn GSM7982885   source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing Burned Larval Zebrafish 24 hours post burn FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix Whole blood Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer. Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator. tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn GSM7982885 GSM7982885: Burned Larval Zebrafish 24 hours post burn; Danio rerio; RNA Seq GSM7982885 r1 GSM7982885 1 Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP479046   loader:fastq load.py Burn-24hpb_S2_L002_R2_001.fastq.gz Burn-24hpb_S2_L002_R1_001.fastq.gz fastq fastq 9861989202.0 84290506.0 GSM7982885 r2 0:28 1:89 A:2769268861;C:2158644227;G:2263475493;T:2669311436;N:1289185 28 89     2769268861 2158644227 2263475493 2669311436 1289185 SRX22969962 SRS19936064 SRA1772557 University of Wisconsin-Madison University of Wisconsin-Madison 2 0.0076 0.9197 0.00232 0.16162 0.98995 0.82852 0.43786 0.55256 28 89 T B sc-like readlen illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United States 2023-12-19 Multi-stage Multi-stage Blood Hematopoietic System
29179 29179 SRR27292308 SRX22969961 SRS19936062 SRP479046 PRJNA1054617 Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish GSE250610 Transcriptome Analysis Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…   pubmed:38922186   Burned Larval Zebrafish 6 hours post burn GSM7982884   source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing Burned Larval Zebrafish 6 hours post burn FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix Whole blood Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer. Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator. tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn GSM7982884 GSM7982884: Burned Larval Zebrafish 6 hours post burn; Danio rerio; RNA Seq GSM7982884 r1 GSM7982884 1 Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP479046   loader:fastq load.py Burn-6hpb_S7_L001_R1_001.fastq.gz Burn-6hpb_S7_L001_R2_001.fastq.gz fastq fastq 12475938384.0 106631952.0 GSM7982884 r1 0:28 1:89 A:3401989108;C:2878275107;G:3114945415;T:3078525361;N:2203393 28 89     3401989108 2878275107 3114945415 3078525361 2203393 SRX22969961 SRS19936062 SRA1772557 University of Wisconsin-Madison University of Wisconsin-Madison 2 0.01053 0.89396 0.00429 0.18315 0.99458 0.85756 0.34876 0.58728 28 89 T B sc-like readlen illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United States 2023-12-19 Multi-stage Multi-stage Blood Hematopoietic System
29180 29180 SRR27292309 SRX22969961 SRS19936062 SRP479046 PRJNA1054617 Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish GSE250610 Transcriptome Analysis Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…   pubmed:38922186   Burned Larval Zebrafish 6 hours post burn GSM7982884   source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn|geo loc name:missing|collection date:missing Burned Larval Zebrafish 6 hours post burn FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix Whole blood Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer. Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator. tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Burn GSM7982884 GSM7982884: Burned Larval Zebrafish 6 hours post burn; Danio rerio; RNA Seq GSM7982884 r1 GSM7982884 1 Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP479046   loader:fastq load.py Burn-6hpb_S7_L002_R1_001.fastq.gz Burn-6hpb_S7_L002_R2_001.fastq.gz fastq fastq 11874083247.0 101487891.0 GSM7982884 r2 0:28 1:89 A:3243501055;C:2735412615;G:2958387721;T:2936117380;N:664476 28 89     3243501055 2735412615 2958387721 2936117380 664476 SRX22969961 SRS19936062 SRA1772557 University of Wisconsin-Madison University of Wisconsin-Madison 2 0.01063 0.89389 0.00439 0.18047 0.99403 0.85878 0.36393 0.54831 28 89 T B sc-like readlen illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United States 2023-12-19 Multi-stage Multi-stage Blood Hematopoietic System
29181 29181 SRR27292310 SRX22969960 SRS19936061 SRP479046 PRJNA1054617 Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish GSE250610 Transcriptome Analysis Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…   pubmed:38922186   Unwounded Larval Zebrafish 5 dpf GSM7982883   source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing Unwounded Larval Zebrafish 5 dpf FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix Whole blood Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer. Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator. tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded GSM7982883 GSM7982883: Unwounded Larval Zebrafish 5 dpf Danio rerio; RNA Seq GSM7982883 r1 GSM7982883 1 Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP479046   loader:fastq load.py WT-5dpf_S6_L001_R2_001.fastq.gz WT-5dpf_S6_L001_R1_001.fastq.gz fastq fastq 31813158312.0 271907336.0 GSM7982883 r1 0:28 1:89 A:8991313503;C:6911976524;G:7105775004;T:8798521232;N:5572049 28 89     8991313503 6911976524 7105775004 8798521232 5572049 SRX22969960 SRS19936061 SRA1772557 University of Wisconsin-Madison University of Wisconsin-Madison 2 0.00661 0.92343 0.00245 0.19293 0.99255 0.81379 0.35935 0.54818 28 89 T B sc-like readlen illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United States 2023-12-19 Multi-stage Multi-stage Blood Hematopoietic System
29182 29182 SRR27292311 SRX22969960 SRS19936061 SRP479046 PRJNA1054617 Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish GSE250610 Transcriptome Analysis Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…   pubmed:38922186   Unwounded Larval Zebrafish 5 dpf GSM7982883   source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing Unwounded Larval Zebrafish 5 dpf FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix Whole blood Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer. Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator. tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded GSM7982883 GSM7982883: Unwounded Larval Zebrafish 5 dpf Danio rerio; RNA Seq GSM7982883 r1 GSM7982883 1 Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP479046   loader:fastq load.py WT-5dpf_S6_L002_R1_001.fastq.gz WT-5dpf_S6_L002_R2_001.fastq.gz fastq fastq 30524386113.0 260892189.0 GSM7982883 r2 0:28 1:89 A:8637605077;C:6625244702;G:6807369409;T:8452468968;N:1697957 28 89     8637605077 6625244702 6807369409 8452468968 1697957 SRX22969960 SRS19936061 SRA1772557 University of Wisconsin-Madison University of Wisconsin-Madison 2 0.00648 0.92418 0.00233 0.19549 0.99241 0.81444 0.37733 0.54674 28 89 T B sc-like readlen illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United States 2023-12-19 Multi-stage Multi-stage Blood Hematopoietic System
29183 29183 SRR27292312 SRX22969959 SRS19936060 SRP479046 PRJNA1054617 Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish GSE250610 Transcriptome Analysis Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…   pubmed:38922186   Unwounded Larval Zebrafish 4 dpf GSM7982882   source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing Unwounded Larval Zebrafish 4 dpf FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix Whole blood Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer. Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator. tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded GSM7982882 GSM7982882: Unwounded Larval Zebrafish 4 dpf Danio rerio; RNA Seq GSM7982882 r1 GSM7982882 1 Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP479046   loader:fastq load.py WT-4dpf_S1_L001_R1_001.fastq.gz WT-4dpf_S1_L001_R2_001.fastq.gz fastq fastq 12682286721.0 108395613.0 GSM7982882 r1 0:28 1:89 A:3575375325;C:2777398557;G:2900088646;T:3425909511;N:3514682 28 89     3575375325 2777398557 2900088646 3425909511 3514682 SRX22969959 SRS19936060 SRA1772557 University of Wisconsin-Madison University of Wisconsin-Madison 2 0.00505 0.92112 0.00185 0.16865 0.99257 0.8258 0.38216 0.5512 28 89 T B sc-like readlen illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United States 2023-12-19 Multi-stage Multi-stage Blood Hematopoietic System
29184 29184 SRR27292313 SRX22969959 SRS19936060 SRP479046 PRJNA1054617 Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish GSE250610 Transcriptome Analysis Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…   pubmed:38922186   Unwounded Larval Zebrafish 4 dpf GSM7982882   source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing Unwounded Larval Zebrafish 4 dpf FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix Whole blood Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer. Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator. tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded GSM7982882 GSM7982882: Unwounded Larval Zebrafish 4 dpf Danio rerio; RNA Seq GSM7982882 r1 GSM7982882 1 Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP479046   loader:fastq load.py WT-4dpf_S1_L002_R2_001.fastq.gz WT-4dpf_S1_L002_R1_001.fastq.gz fastq fastq 12832453413.0 109679089.0 GSM7982882 r2 0:28 1:89 A:3620789787;C:2810897812;G:2929508681;T:3469577031;N:1680102 28 89     3620789787 2810897812 2929508681 3469577031 1680102 SRX22969959 SRS19936060 SRA1772557 University of Wisconsin-Madison University of Wisconsin-Madison 2 0.0052 0.92355 0.00192 0.16775 0.99263 0.8253 0.37089 0.55115 28 89 T B sc-like readlen illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United States 2023-12-19 Multi-stage Multi-stage Blood Hematopoietic System
29185 29185 SRR27292314 SRX22969958 SRS19936059 SRP479046 PRJNA1054617 Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish GSE250610 Transcriptome Analysis Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…   pubmed:38922186   Unwounded Larval Zebrafish 3 dpf GSM7982881   source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing Unwounded Larval Zebrafish 3 dpf FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix Whole blood Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer. Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator. tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded GSM7982881 GSM7982881: Unwounded Larval Zebrafish 3 dpf Danio rerio; RNA Seq GSM7982881 r1 GSM7982881 1 Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP479046   loader:fastq load.py WT-3dpf_S4_L001_R1_001.fastq.gz WT-3dpf_S4_L001_R2_001.fastq.gz fastq fastq 7586138430.0 64838790.0 GSM7982881 r1 0:28 1:89 A:2101749534;C:1692875352;G:1784872358;T:2005308370;N:1332816 28 89     2101749534 1692875352 1784872358 2005308370 1332816 SRX22969958 SRS19936059 SRA1772557 University of Wisconsin-Madison University of Wisconsin-Madison 2 0.00976 0.92096 0.00368 0.18077 0.99356 0.83875 0.3661 0.59073 28 89 T B sc-like readlen illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United States 2023-12-19 Multi-stage Multi-stage Blood Hematopoietic System
29186 29186 SRR27292315 SRX22969958 SRS19936059 SRP479046 PRJNA1054617 Modeling Neutrophil Heterogeneity Contribution to Burn Healing in Larval Zebrafish GSE250610 Transcriptome Analysis Neutrophils accumulate early in burn wounds and their activation is associated with more severe burns. Understanding their functionality would facilitate the development of a more targeted therapeutic strategy for healing. However we still lack a view of the cellular and functional heterogeneity in neutrophils involved in thermal injuries. Here we establish the use of larval zebrafish for understanding neutrophil responses in burn. Zebrafish model allows for linking neutrophil states and their functions in real time through genetic modifications and live imaging. We performed single cell transcriptional scRNA Seq mapping of myeloid cells during a 3 day time course in burn and unwounded conditions. We identified transcriptionally distinct states in myeloid cells that form a consistent population structure across time points and conditions. By comparing burn and unwounded conditions we found subtype specific enrichment of biological processes and differential usage of gene regulatory networks. Pseudotime and RNA velocity analyses predict distinct branched trajectories for neutrophils with one branch resembling the process of human neutrophil maturation. The other branch is not transcriptionally conserved with humans and is highly associated with leukocyte migration functionality suggesting its engagement at the wound site. Transcriptional network analysis identified RAR/RXR family transcription factors as potential upstream factors driving this trajectory divergence in neutrophils. Furthermore we characterized the transcriptional dynamics of cell cell interactions in both conditions by time. Among burn induced signaling pathways we found il6 il6r signaling as a time point specific macrophage neutrophil interaction suggesting the importance of timing in innate immune response in burn. Finally to test the translational value of our fish model we examined zebrafish neutrophil state signatures in human burn patient samples. We found homolog expression of immature neutrophils positively correlates with the de…   pubmed:38922186   Unwounded Larval Zebrafish 3 dpf GSM7982881   source name:Whole blood|tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded|geo loc name:missing|collection date:missing Unwounded Larval Zebrafish 3 dpf FASTQ files were aligned to Zebrafish genome using cellranger version v3.1.1 Unwounded 4days Burn 24 hours v6.1.2 Unwounded 3days Unwounded 5days Burn 6hours Burn 48hours UMI cutoffs per droplet were calcuated from cellranger and filtered feature matrices were used to generate a Seurat object V4 Assembly: GRCz11 danRer11 Supplementary files format and content: RNA count matrix Whole blood Larval zebrafish were wounded on the tail fin region at 3 days post feritlization using a handheld cauterizer. Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing Zebrafish embroys were collected from adult Tgmpx:dendra mpeg1.1:mCherry fish and kept in E3 medium with 1% methylene blue inside a 28.5˚C incubator. tissue:Whole blood|cell type:Macrophage|cell type:Neutrophil|genotype:WT|treatment:Unwounded GSM7982881 GSM7982881: Unwounded Larval Zebrafish 3 dpf Danio rerio; RNA Seq GSM7982881 r1 GSM7982881 1 Dissociated cells were sorted using fluorescence activated cell sorting using BD FACSAria to separate neutrophils and macrophages. Cells were then loaded into the 10x chromium controller for GEM encapsulation and reverse transcription per manufacturer's instructions. Library construction was performed per 10x instructions with three prime v2 chemistry Each prepared library was sequenced on the NovaSeq using dual index sequencing   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP479046   loader:fastq load.py WT-3dpf_S4_L002_R1_001.fastq.gz WT-3dpf_S4_L002_R2_001.fastq.gz fastq fastq 7258692168.0 62040104.0 GSM7982881 r2 0:28 1:89 A:2013529524;C:1617959197;G:1704796898;T:1922004726;N:401823 28 89     2013529524 1617959197 1704796898 1922004726 401823 SRX22969958 SRS19936059 SRA1772557 University of Wisconsin-Madison University of Wisconsin-Madison 2 0.00949 0.92207 0.00359 0.18081 0.99375 0.83751 0.37347 0.55889 28 89 T B sc-like readlen illumina novaseq_era unknown random_priming unknown sc single_cell_droplet 10x   United States 2023-12-19 Multi-stage Multi-stage Blood Hematopoietic System
30018 30018 SRR27988043 SRX23641260 SRS20476222 SRP485064 PRJNA1067370 zebrafish embryo for scRNA seq and bulk RNA seq PRJNA1067370 Other Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.       hamp / 36 hpf blood zebrafish hamp / 36 hpf blood replicate 3   strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:hamp knockdown|sample type:tissue sample|treatment:replicate 3|BioSampleModel:Model organism or animal                 RNA seq hamp / 36 hpf blood replicate 3 B 6 B 6 bulk RNA seq     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485064     KO-3_R2_001.fastq.gz KO-3_R1_001.fastq.gz fastq fastq 8752665900.0 29175553.0 KO 3 R1 001.fastq.gz 0:150 1:150 A:2204170575;C:2174083961;G:2224694970;T:2149603712;N:112682 150 150     2204170575 2174083961 2224694970 2149603712 112682 SRX23641260 SRS20476222 SRA1803422 Shanghai Ocean University|College of Fisheries and Life Shanghai Ocean University 2 0.91553 0.91645 0.01276 0.01288 0.85884 0.85839 0.35101 0.40996 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc_generic bulk bulk   China 2024-02-16 Pharyngula Embryo Blood Hematopoietic System
30019 30019 SRR27988044 SRX23641259 SRS20476221 SRP485064 PRJNA1067370 zebrafish embryo for scRNA seq and bulk RNA seq PRJNA1067370 Other Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.       hamp / 36 hpf blood zebrafish hamp / 36 hpf blood replicate 2   strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:hamp knockdown|sample type:tissue sample|treatment:replicate 2|BioSampleModel:Model organism or animal                 RNA seq hamp / 36 hpf blood replicate 2 B 5 B 5 bulk RNA seq     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485064     KO-2_R1_001.fastq.gz KO-2_R2_001.fastq.gz fastq fastq 8060498700.0 26868329.0 KO 2 R1 001.fastq.gz 0:150 1:150 A:2045797336;C:1985847523;G:2035528018;T:1993222840;N:102983 150 150     2045797336 1985847523 2035528018 1993222840 102983 SRX23641259 SRS20476221 SRA1803422 Shanghai Ocean University|College of Fisheries and Life Shanghai Ocean University 2 0.9213 0.92027 0.0167 0.01676 0.8242 0.82475 0.41081 0.41111 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc_generic bulk bulk   China 2024-02-16 Pharyngula Embryo Blood Hematopoietic System
30020 30020 SRR27988045 SRX23641258 SRS20476220 SRP485064 PRJNA1067370 zebrafish embryo for scRNA seq and bulk RNA seq PRJNA1067370 Other Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.       hamp / 36 hpf blood zebrafish hamp / 36 hpf blood replicate 1   strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:hamp knockdown|sample type:tissue sample|treatment:replicate 1|BioSampleModel:Model organism or animal                 RNA seq hamp / 36 hpf blood replicate 1 B 4 B 4 bulk RNA seq     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485064     KO-1_R1_001.fastq.gz KO-1_R2_001.fastq.gz fastq fastq 8707637700.0 29025459.0 KO 1 R1 001.fastq.gz 0:150 1:150 A:2222026435;C:2133480283;G:2182087972;T:2169932447;N:110563 150 150     2222026435 2133480283 2182087972 2169932447 110563 SRX23641258 SRS20476220 SRA1803422 Shanghai Ocean University|College of Fisheries and Life Shanghai Ocean University 2 0.91531 0.91359 0.02185 0.0221 0.81213 0.8128 0.37868 0.42351 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc_generic bulk bulk   China 2024-02-16 Pharyngula Embryo Blood Hematopoietic System
30021 30021 SRR27988046 SRX23641257 SRS20476219 SRP485064 PRJNA1067370 zebrafish embryo for scRNA seq and bulk RNA seq PRJNA1067370 Other Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.       wild type 36 hpf blood zebrafish wild type 36 hpf blood replicate 3   strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:wild type|sample type:tissue sample|treatment:replicate 3|BioSampleModel:Model organism or animal                 RNA seq wild type 36 hpf blood replicate 3 B 3 B 3 bulk RNA seq     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485064     WT-3_R1_001.fastq.gz WT-3_R2_001.fastq.gz fastq fastq 8829371400.0 29431238.0 WT 3 R1 001.fastq.gz 0:150 1:150 A:2278837675;C:2141723937;G:2193442375;T:2215253519;N:113894 150 150     2278837675 2141723937 2193442375 2215253519 113894 SRX23641257 SRS20476219 SRA1803422 Shanghai Ocean University|College of Fisheries and Life Shanghai Ocean University 2 0.90531 0.9043 0.03015 0.03017 0.8101 0.8112 0.43085 0.43002 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc_generic bulk bulk   China 2024-02-16 Pharyngula Embryo Blood Hematopoietic System
30022 30022 SRR27988047 SRX23641256 SRS20476218 SRP485064 PRJNA1067370 zebrafish embryo for scRNA seq and bulk RNA seq PRJNA1067370 Other Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.       wild type 36 hpf blood zebrafish wild type 36 hpf blood replicate 2   strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:wild type|sample type:tissue sample|treatment:replicate 2|BioSampleModel:Model organism or animal                 RNA seq wild type 36 hpf blood replicate 2 B 2 B 2 bulk RNA seq     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485064     WT-2_R1_001.fastq.gz WT-2_R2_001.fastq.gz fastq fastq 7365643800.0 24552146.0 WT 2 R1 001.fastq.gz 0:150 1:150 A:1867985067;C:1819016430;G:1870006707;T:1808540769;N:94827 150 150     1867985067 1819016430 1870006707 1808540769 94827 SRX23641256 SRS20476218 SRA1803422 Shanghai Ocean University|College of Fisheries and Life Shanghai Ocean University 2 0.90612 0.90536 0.01714 0.01746 0.88109 0.88156 0.32469 0.39232 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc_generic bulk bulk   China 2024-02-16 Pharyngula Embryo Blood Hematopoietic System
30023 30023 SRR27988048 SRX23641255 SRS20476217 SRP485064 PRJNA1067370 zebrafish embryo for scRNA seq and bulk RNA seq PRJNA1067370 Other Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.       wild type 36 hpf blood zebrafish wild type 36 hpf blood replicate 1   strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:wild type|sample type:tissue sample|treatment:replicate 1|BioSampleModel:Model organism or animal                 RNA seq wild type 36 hpf blood replicate 1 B 1 B 1 bulk RNA seq     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485064     WT-1_R1_001.fastq.gz WT-1_R2_001.fastq.gz fastq fastq 8631863400.0 28772878.0 WT 1 R1 001.fastq.gz 0:150 1:150 A:2186212554;C:2135990723;G:2179142081;T:2130408485;N:109557 150 150     2186212554 2135990723 2179142081 2130408485 109557 SRX23641255 SRS20476217 SRA1803422 Shanghai Ocean University|College of Fisheries and Life Shanghai Ocean University 2 0.90461 0.90281 0.01388 0.01365 0.83871 0.83895 0.36511 0.41074 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown sc_generic bulk bulk   China 2024-02-16 Pharyngula Embryo Blood Hematopoietic System
30066 30066 SRR27676305 SRX23343658 SRS20205511 SRP485121 PRJNA1067443 RNA seq&smart seq&CUT TAG PRJNA1067443 Other RNA seq&amp;smart seq&amp;CUT TAG         smart seq of setdb1b mt 2   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:96hpf|collection date:missing|geo loc name:missing|sex:pooled male and female|tissue:hematopoietic stem and progenitor cell|replicate:replicate = biological replicate 2|id</u><u>:9</u><u>|BioSampleModel:Model organism or animal                 smart seq of setdb1b mt 2 smart seq of setdb1b mt 2 smart seq of setdb1b mt 2 smart seq of setdb1b mt of replicate 2     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485121     smart-seq of setdb1b mt_2_R2.fastq.gz.gz smart-seq of setdb1b mt_2_R1.fastq.gz.gz fastq fastq 11957458200.0 39858194.0 smart seq of setdb1b mt 2 R1.fastq.gz.gz 0:150 1:150 A:3692371435;C:1893324720;G:2810967928;T:3560751613;N:42504 150 150     3692371435 1893324720 2810967928 3560751613 42504 SRX23343658 SRS20205511 SRA1789215 East China Normal University|Institute of Biomedical Sciences East China Normal University 2 0.76332 0.82639 0.22191 0.23939 0.87093 0.87117 0.59757 0.60008 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-22 Larval Larval Blood Hematopoietic System
30067 30067 SRR27676306 SRX23343657 SRS20205510 SRP485121 PRJNA1067443 RNA seq&smart seq&CUT TAG PRJNA1067443 Other RNA seq&amp;smart seq&amp;CUT TAG         smart seq of setdb1b mt 1   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:96hpf|collection date:missing|geo loc name:missing|sex:pooled male and female|tissue:hematopoietic stem and progenitor cell|replicate:replicate = biological replicate 1|id</u><u>:8</u><u>|BioSampleModel:Model organism or animal                 smart seq of setdb1b mt 1 smart seq of setdb1b mt 1 smart seq of setdb1b mt 1 smart seq of setdb1b mt of replicate 1     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485121     smart-seq of setdb1b mt_1_R1.fastq.gz.gz smart-seq of setdb1b mt_1_R2.fastq.gz.gz fastq fastq 9537788700.0 31792629.0 smart seq of setdb1b mt 1 R1.fastq.gz.gz 0:150 1:150 A:3044433376;C:1450924984;G:2142347814;T:2900047705;N:34821 150 150     3044433376 1450924984 2142347814 2900047705 34821 SRX23343657 SRS20205510 SRA1789215 East China Normal University|Institute of Biomedical Sciences East China Normal University 2 0.74808 0.79354 0.21148 0.22263 0.87405 0.87545 0.58431 0.58836 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-22 Larval Larval Blood Hematopoietic System
30068 30068 SRR27676307 SRX23343656 SRS20205509 SRP485121 PRJNA1067443 RNA seq&smart seq&CUT TAG PRJNA1067443 Other RNA seq&amp;smart seq&amp;CUT TAG         smart seq of setdb1b control 2   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:96hpf|collection date:missing|geo loc name:missing|sex:pooled male and female|tissue:hematopoietic stem and progenitor cell|replicate:replicate = biological replicate 2|id</u><u>:7</u><u>|BioSampleModel:Model organism or animal                 smart seq of setdb1b control 2 smart seq of setdb1b control 2 smart seq of setdb1b control 2 smart seq of setdb1b control of replicate 2     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485121     smart-seq of setdb1b control_2_R1.fastq.gz.gz smart-seq of setdb1b control_2_R2.fastq.gz.gz fastq fastq 7963596600.0 26545322.0 smart seq of setdb1b control 2 R1.fastq.gz.gz 0:150 1:150 A:2522387513;C:1217203824;G:1776725064;T:2447251088;N:29111 150 150     2522387513 1217203824 1776725064 2447251088 29111 SRX23343656 SRS20205509 SRA1789215 East China Normal University|Institute of Biomedical Sciences East China Normal University 2 0.77121 0.80578 0.22631 0.23757 0.85953 0.86298 0.58219 0.58387 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-22 Larval Larval Blood Hematopoietic System
30069 30069 SRR27676308 SRX23343655 SRS20205508 SRP485121 PRJNA1067443 RNA seq&smart seq&CUT TAG PRJNA1067443 Other RNA seq&amp;smart seq&amp;CUT TAG         smart seq of setdb1b control 1   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:96hpf|collection date:missing|geo loc name:missing|sex:pooled male and female|tissue:hematopoietic stem and progenitor cell|replicate:replicate = biological replicate 1|id</u><u>:6</u><u>|BioSampleModel:Model organism or animal                 smart seq of setdb1b control 1 smart seq of setdb1b control 1 smart seq of setdb1b control 1 smart seq of setdb1b control of replicate 1     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485121     smart-seq of setdb1b control_1_R2.fastq.gz.gz smart-seq of setdb1b control_1_R1.fastq.gz.gz fastq fastq 11867370900.0 39557903.0 smart seq of setdb1b control 1 R1.fastq.gz.gz 0:150 1:150 A:3969636478;C:1678555005;G:2520767064;T:3698368678;N:43675 150 150     3969636478 1678555005 2520767064 3698368678 43675 SRX23343655 SRS20205508 SRA1789215 East China Normal University|Institute of Biomedical Sciences East China Normal University 2 0.73517 0.73836 0.23036 0.23129 0.86407 0.86675 0.59652 0.59533 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-22 Larval Larval Blood Hematopoietic System
30070 30070 SRR27676309 SRX23343654 SRS20205505 SRP485121 PRJNA1067443 RNA seq&smart seq&CUT TAG PRJNA1067443 Other RNA seq&amp;smart seq&amp;CUT TAG         RNA seq of atf7ip mt 2   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72hpf|collection date:missing|geo loc name:missing|sex:pooled male and female|tissue:hematopoietic stem and progenitor cell|replicate:replicate = biological replicate 2|id</u><u>:5</u><u>|BioSampleModel:Model organism or animal                 mRNAseq of atf7ip mt RNA seq of atf7ip mt 2 RNA seq of atf7ip mt 2 mRNAseq of atf7ip mt of replicate 2     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485121     RNA-seq of atf7ip mt_2_R2.fastq.gz.gz RNA-seq of atf7ip mt_2_R1.fastq.gz.gz fastq fastq 2881485000.0 9604950.0 RNA seq of atf7ip mt 2 R1.fastq.gz.gz 0:150 1:150 A:714870764;C:672086586;G:819085358;T:675370688;N:71604 150 150     714870764 672086586 819085358 675370688 71604 SRX23343654 SRS20205505 SRA1789215 East China Normal University|Institute of Biomedical Sciences East China Normal University 2 0.95105 0.94782 0.0877 0.08683 0.67838 0.68085 0.4943 0.49308 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-22 Larval Larval Blood Hematopoietic System
30071 30071 SRR27676310 SRX23343653 SRS20205506 SRP485121 PRJNA1067443 RNA seq&smart seq&CUT TAG PRJNA1067443 Other RNA seq&amp;smart seq&amp;CUT TAG         RNA seq of atf7ip mt 1   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72hpf|collection date:missing|geo loc name:missing|sex:pooled male and female|tissue:hematopoietic stem and progenitor cell|replicate:replicate = biological replicate 1|id</u><u>:4</u><u>|BioSampleModel:Model organism or animal                 mRNAseq of atf7ip mt RNA seq of atf7ip mt 1 RNA seq of atf7ip mt 1 mRNAseq of atf7ip mt of replicate 1     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485121     RNA-seq of atf7ip mt_1_R2.fastq.gz.gz RNA-seq of atf7ip mt_1_R1.fastq.gz.gz fastq fastq 5215476900.0 17384923.0 RNA seq of atf7ip mt 1 R1.fastq.gz.gz 0:150 1:150 A:1305694077;C:1250588317;G:1437727006;T:1221425310;N:42190 150 150     1305694077 1250588317 1437727006 1221425310 42190 SRX23343653 SRS20205506 SRA1789215 East China Normal University|Institute of Biomedical Sciences East China Normal University 2 0.95459 0.9546 0.09418 0.0933 0.67353 0.67643 0.49356 0.49989 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-22 Larval Larval Blood Hematopoietic System
30072 30072 SRR27676311 SRX23343652 SRS20205507 SRP485121 PRJNA1067443 RNA seq&smart seq&CUT TAG PRJNA1067443 Other RNA seq&amp;smart seq&amp;CUT TAG         RNA seq of atf7ip control 3   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72hpf|collection date:missing|geo loc name:missing|sex:pooled male and female|tissue:hematopoietic stem and progenitor cell|replicate:replicate = biological replicate 3|id</u><u>:3</u><u>|BioSampleModel:Model organism or animal                 mRNAseq of atf7ip control RNA seq of atf7ip control 3 RNA seq of atf7ip control 3 mRNAseq of atf7ip control of replicate 3     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485121     RNA-seq of atf7ip control_3_R2.fastq.gz.gz RNA-seq of atf7ip control_3_R1.fastq.gz.gz fastq fastq 6742549200.0 22475164.0 RNA seq of atf7ip control 3 R1.fastq.gz.gz 0:150 1:150 A:1698977237;C:1657996046;G:1800441072;T:1584967439;N:167406 150 150     1698977237 1657996046 1800441072 1584967439 167406 SRX23343652 SRS20205507 SRA1789215 East China Normal University|Institute of Biomedical Sciences East China Normal University 2 0.96114 0.9601 0.05191 0.05152 0.69219 0.69398 0.48597 0.48633 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-22 Larval Larval Blood Hematopoietic System
30073 30073 SRR27676312 SRX23343651 SRS20205504 SRP485121 PRJNA1067443 RNA seq&smart seq&CUT TAG PRJNA1067443 Other RNA seq&amp;smart seq&amp;CUT TAG         RNA seq of atf7ip control 2   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72hpf|collection date:missing|geo loc name:missing|sex:pooled male and female|tissue:hematopoietic stem and progenitor cell|replicate:replicate = biological replicate 2|id</u><u>:2</u><u>|BioSampleModel:Model organism or animal                 mRNAseq of atf7ip control RNA seq of atf7ip control 2 RNA seq of atf7ip control 2 mRNAseq of atf7ip control of replicate 2     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485121     RNA-seq of atf7ip control_2_R2.fastq.gz.gz RNA-seq of atf7ip control_2_R1.fastq.gz.gz fastq fastq 6962540400.0 23208468.0 RNA seq of atf7ip control 2 R1.fastq.gz.gz 0:150 1:150 A:1794934846;C:1640272261;G:1855642638;T:1671491013;N:199642 150 150     1794934846 1640272261 1855642638 1671491013 199642 SRX23343651 SRS20205504 SRA1789215 East China Normal University|Institute of Biomedical Sciences East China Normal University 2 0.95531 0.95468 0.05949 0.05926 0.71019 0.71129 0.50401 0.50622 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-22 Larval Larval Blood Hematopoietic System
30074 30074 SRR27676313 SRX23343650 SRS20205503 SRP485121 PRJNA1067443 RNA seq&smart seq&CUT TAG PRJNA1067443 Other RNA seq&amp;smart seq&amp;CUT TAG         RNA seq of atf7ip control 1   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72hpf|collection date:missing|geo loc name:missing|sex:pooled male and female|tissue:hematopoietic stem and progenitor cell|replicate:replicate = biological replicate 1|id</u><u>:1</u><u>|BioSampleModel:Model organism or animal                 mRNAseq of atf7ip control RNA seq of atf7ip control 1 RNA seq of atf7ip control 1 mRNAseq of atf7ip control of replicate 1     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP485121     RNA-seq of atf7ip control_1_R1.fastq.gz.gz RNA-seq of atf7ip control_1_R2.fastq.gz.gz fastq fastq 8543359800.0 28477866.0 RNA seq of atf7ip control 1 R1.fastq.gz.gz 0:150 1:150 A:2200058170;C:2049588985;G:2219737118;T:2073765388;N:210139 150 150     2200058170 2049588985 2219737118 2073765388 210139 SRX23343650 SRS20205503 SRA1789215 East China Normal University|Institute of Biomedical Sciences East China Normal University 2 0.96026 0.95618 0.05646 0.05613 0.68424 0.6856 0.48963 0.49334 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-22 Larval Larval Blood Hematopoietic System
31522 31522 SRR28418937 SRX24023264 SRS20817617 SRP497230 PRJNA1090848 Reprogramming of 3D genome structure underlying HSPC development in zebrafish [RNA seq] GSE262188 Transcriptome Analysis Development of hematopoietic stem and progenitor cells HSPC is a multi staged complex process that conserved between zebrafish and mammals; however the mechanism underlying HSPC development is not fully understood. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision its dynamic and role in HSPC development is poorly investigated. Here we performed chromatin structure and multi omics dissection across different stages of HSPC developmental trajectory in zebrafish. Chromatin organization of zebrafish HSPC resemble mammalian cells with similar hierarchical structure and characteristics. We revealed the multi scale reorganization of 3D genome and its influence on transcriptional regulation and transition of cell function during HSPC development. Nascent HSPC is featured by loose conformation with obscure structure at all layers. Notably PU.1 was identified as a potential factor mediating formation of promoter involved loops and regulating gene expression as well as HSPC function. Our results provided a global view of chromatin structure dynamics associated with development of zebrafish HSPC and discovered key transcription factor involved in HSPC chromatin interactions which will provide new insights into the epigenetic regulatory mechanisms underlying vertebrate HSPC fate decision. Overall design: To comprehensively dissect 3D genome rearrangement and its relation to transcriptional changes of zebrafish HSPC we get RNA seq results from adult sample. Then conjoint analysis of RNA seq with other datas can reveal the function of transcriptional factors such as PU.1 .   pubmed:38886858   HPSC rep3 RNA seq 3month GSM8159257   source name:hematopoietic stem cell|tissue:hematopoietic stem cell|cell line:TgCD41:GFP gata1:dsRed|cell type:hematopoietic stem cell|genotype:CD41+gata1 |time:3month|treatment:flow cytometry|geo loc name:missing|collection date:missing HPSC rep3 RNA seq 3month The library is evaluated by FastQC. Readswith mean quality score less than orequal to 30 are removed. Raw reads were trimmed and removed for adapter sequences by fatspv.0.23.2 withpaired end default parameters. Extremely short fragment with length less than or equal to 30bp were also removed. post filtering high quality reads were aligned to GRCz10 zebrafish genome using HISAT2 with default parameters. FeatureCounts wasused to quantify gene expression and obtain reads count. Fold changes in gene transcription levels were estimated using DESeq2.Enrichment analysis of gene function was performed in the Metascape platform. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample hematopoietic stem cell   Briefly ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U RNase inhibitor 10 U dNTP mix 10 mM each SS III first strand buffer 1× DTT 5 mM betaine 1 M MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina   tissue:hematopoietic stem cell|cell line:TgCD41:GFP gata1:dsRed|cell type:hematopoietic stem cell|genotype:CD41+gata1 |time:3month|treatment:flow cytometry GSM8159257 GSM8159257: HPSC rep3 RNA seq 3month; Danio rerio; RNA Seq GSM8159257 r1 GSM8159257 1 Briefly ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U RNase inhibitor 10 U dNTP mix 10 mM each SS III first strand buffer 1× DTT 5 mM betaine 1 M MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP497230   loader:fastq load.py RNA-seq_Adult_HPSC_rep3_R1.fq.gz RNA-seq_Adult_HPSC_rep3_R2.fq.gz fastq fastq 11621758500.0 38739195.0 GSM8159257 r1 0:150 1:150 A:3144084931;C:2632272493;G:2693165513;T:3151802925;N:432638 150 150     3144084931 2632272493 2693165513 3151802925 432638 SRX24023264 SRS20817617 SRA1831889 South China University of Technology South China University of Technology                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-03-21 Adult Adult Blood Hematopoietic System
31523 31523 SRR28418938 SRX24023263 SRS20817616 SRP497230 PRJNA1090848 Reprogramming of 3D genome structure underlying HSPC development in zebrafish [RNA seq] GSE262188 Transcriptome Analysis Development of hematopoietic stem and progenitor cells HSPC is a multi staged complex process that conserved between zebrafish and mammals; however the mechanism underlying HSPC development is not fully understood. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision its dynamic and role in HSPC development is poorly investigated. Here we performed chromatin structure and multi omics dissection across different stages of HSPC developmental trajectory in zebrafish. Chromatin organization of zebrafish HSPC resemble mammalian cells with similar hierarchical structure and characteristics. We revealed the multi scale reorganization of 3D genome and its influence on transcriptional regulation and transition of cell function during HSPC development. Nascent HSPC is featured by loose conformation with obscure structure at all layers. Notably PU.1 was identified as a potential factor mediating formation of promoter involved loops and regulating gene expression as well as HSPC function. Our results provided a global view of chromatin structure dynamics associated with development of zebrafish HSPC and discovered key transcription factor involved in HSPC chromatin interactions which will provide new insights into the epigenetic regulatory mechanisms underlying vertebrate HSPC fate decision. Overall design: To comprehensively dissect 3D genome rearrangement and its relation to transcriptional changes of zebrafish HSPC we get RNA seq results from adult sample. Then conjoint analysis of RNA seq with other datas can reveal the function of transcriptional factors such as PU.1 .   pubmed:38886858   HPSC rep2 RNA seq 3month GSM8159256   source name:hematopoietic stem cell|tissue:hematopoietic stem cell|cell line:TgCD41:GFP gata1:dsRed|cell type:hematopoietic stem cell|genotype:CD41+gata1 |time:3month|treatment:flow cytometry|geo loc name:missing|collection date:missing HPSC rep2 RNA seq 3month The library is evaluated by FastQC. Readswith mean quality score less than orequal to 30 are removed. Raw reads were trimmed and removed for adapter sequences by fatspv.0.23.2 withpaired end default parameters. Extremely short fragment with length less than or equal to 30bp were also removed. post filtering high quality reads were aligned to GRCz10 zebrafish genome using HISAT2 with default parameters. FeatureCounts wasused to quantify gene expression and obtain reads count. Fold changes in gene transcription levels were estimated using DESeq2.Enrichment analysis of gene function was performed in the Metascape platform. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample hematopoietic stem cell   Briefly ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U RNase inhibitor 10 U dNTP mix 10 mM each SS III first strand buffer 1× DTT 5 mM betaine 1 M MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina   tissue:hematopoietic stem cell|cell line:TgCD41:GFP gata1:dsRed|cell type:hematopoietic stem cell|genotype:CD41+gata1 |time:3month|treatment:flow cytometry GSM8159256 GSM8159256: HPSC rep2 RNA seq 3month; Danio rerio; RNA Seq GSM8159256 r1 GSM8159256 1 Briefly ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U RNase inhibitor 10 U dNTP mix 10 mM each SS III first strand buffer 1× DTT 5 mM betaine 1 M MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP497230   loader:fastq load.py RNA-seq_Adult_HPSC_rep2_R1.fq.gz RNA-seq_Adult_HPSC_rep2_R2.fq.gz fastq fastq 9951217200.0 33170724.0 GSM8159256 r1 0:150 1:150 A:2755384814;C:2209586340;G:2237522365;T:2748523249;N:200432 150 150     2755384814 2209586340 2237522365 2748523249 200432 SRX24023263 SRS20817616 SRA1831889 South China University of Technology South China University of Technology                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-03-21 Adult Adult Blood Hematopoietic System
31524 31524 SRR28418939 SRX24023262 SRS20817615 SRP497230 PRJNA1090848 Reprogramming of 3D genome structure underlying HSPC development in zebrafish [RNA seq] GSE262188 Transcriptome Analysis Development of hematopoietic stem and progenitor cells HSPC is a multi staged complex process that conserved between zebrafish and mammals; however the mechanism underlying HSPC development is not fully understood. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision its dynamic and role in HSPC development is poorly investigated. Here we performed chromatin structure and multi omics dissection across different stages of HSPC developmental trajectory in zebrafish. Chromatin organization of zebrafish HSPC resemble mammalian cells with similar hierarchical structure and characteristics. We revealed the multi scale reorganization of 3D genome and its influence on transcriptional regulation and transition of cell function during HSPC development. Nascent HSPC is featured by loose conformation with obscure structure at all layers. Notably PU.1 was identified as a potential factor mediating formation of promoter involved loops and regulating gene expression as well as HSPC function. Our results provided a global view of chromatin structure dynamics associated with development of zebrafish HSPC and discovered key transcription factor involved in HSPC chromatin interactions which will provide new insights into the epigenetic regulatory mechanisms underlying vertebrate HSPC fate decision. Overall design: To comprehensively dissect 3D genome rearrangement and its relation to transcriptional changes of zebrafish HSPC we get RNA seq results from adult sample. Then conjoint analysis of RNA seq with other datas can reveal the function of transcriptional factors such as PU.1 .   pubmed:38886858   HPSC rep1 RNA seq 3month GSM8159255   source name:hematopoietic stem cell|tissue:hematopoietic stem cell|cell line:TgCD41:GFP gata1:dsRed|cell type:hematopoietic stem cell|genotype:CD41+gata1 |time:3month|treatment:flow cytometry|geo loc name:missing|collection date:missing HPSC rep1 RNA seq 3month The library is evaluated by FastQC. Readswith mean quality score less than orequal to 30 are removed. Raw reads were trimmed and removed for adapter sequences by fatspv.0.23.2 withpaired end default parameters. Extremely short fragment with length less than or equal to 30bp were also removed. post filtering high quality reads were aligned to GRCz10 zebrafish genome using HISAT2 with default parameters. FeatureCounts wasused to quantify gene expression and obtain reads count. Fold changes in gene transcription levels were estimated using DESeq2.Enrichment analysis of gene function was performed in the Metascape platform. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample hematopoietic stem cell   Briefly ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U RNase inhibitor 10 U dNTP mix 10 mM each SS III first strand buffer 1× DTT 5 mM betaine 1 M MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina   tissue:hematopoietic stem cell|cell line:TgCD41:GFP gata1:dsRed|cell type:hematopoietic stem cell|genotype:CD41+gata1 |time:3month|treatment:flow cytometry GSM8159255 GSM8159255: HPSC rep1 RNA seq 3month; Danio rerio; RNA Seq GSM8159255 r1 GSM8159255 1 Briefly ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U RNase inhibitor 10 U dNTP mix 10 mM each SS III first strand buffer 1× DTT 5 mM betaine 1 M MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP497230   loader:fastq load.py RNA-seq_Adult_HPSC_rep1_R1.fq.gz RNA-seq_Adult_HPSC_rep1_R2.fq.gz fastq fastq 11096617200.0 36988724.0 GSM8159255 r1 0:150 1:150 A:3071303610;C:2460399138;G:2510824334;T:3053621175;N:468943 150 150     3071303610 2460399138 2510824334 3053621175 468943 SRX24023262 SRS20817615 SRA1831889 South China University of Technology South China University of Technology                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2024-03-21 Adult Adult Blood Hematopoietic System
35485 35485 SRR32834031 SRX28117245 SRS24473023 SRP572644 PRJNA1241156 Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish GSE292726 Transcriptome Analysis Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.       mCherry cells rag1 crispant R848 treated GSM8864273   tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|genotype:rag1 mosaic mutant|treatment:Resiquimod R848 treated|geo loc name:missing|collection date:missing mCherry cells rag1 crispant R848 treated For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix Hematopoietic & Immune Cells The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used. Larvae were maintained in standard conditions at 28C cell type:Hematopoietic & Immune Cells|genotype:rag1 mosaic mutant|treatment:Resiquimod R848 treated GSM8864273 GSM8864273: mCherry cells rag1 crispant R848 treated; Danio rerio; RNA Seq GSM8864273 r1 GSM8864273 1 Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP572644   loader:fastq load.py|options: readTypes=TBTT read1PairFiles=Rag1 crispant with R848 S64 L005 R1 001.fastq.gz read2PairFiles=Rag1 crispant with R848 S64 L005 R2 001.fastq.gz read3PairFiles=Rag1 crispant with R848 S64 L005 I1 001.fastq.gz read4PairFiles=Rag1 crispant with R848 S64 L005 I2 001.fastq.gz Rag1_crispant_with_R848_S64_L005_I1_001.fastq.gz Rag1_crispant_with_R848_S64_L005_I2_001.fastq.gz Rag1_crispant_with_R848_S64_L005_R1_001.fastq.gz Rag1_crispant_with_R848_S64_L005_R2_001.fastq.gz fastq fastq fastq fastq 51690121264.0 371871376.0 GSM8864273 r1 0:28 1:91 2:10 3:10 A:9268291738;C:7690563124;G:8398909329;T:8480309041;N:2221984 28 91 10 10 9268291738 7690563124 8398909329 8480309041 2221984 SRX28117245 SRS24473023 SRA2098862 Albert Einstein College of Medicine Albert Einstein College of Medicine                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2025-03-24 Larval Larval Blood Hematopoietic System
35486 35486 SRR32834032 SRX28117244 SRS24473025 SRP572644 PRJNA1241156 Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish GSE292726 Transcriptome Analysis Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.       mCherry cells slc24a5 crispant R848 treated GSM8864272   tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|genotype:slc24a5 mosaic mutant|treatment:Resiquimod R848 treated|geo loc name:missing|collection date:missing mCherry cells slc24a5 crispant R848 treated For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix Hematopoietic & Immune Cells The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used. Larvae were maintained in standard conditions at 28C cell type:Hematopoietic & Immune Cells|genotype:slc24a5 mosaic mutant|treatment:Resiquimod R848 treated GSM8864272 GSM8864272: mCherry cells slc24a5 crispant R848 treated; Danio rerio; RNA Seq GSM8864272 r1 GSM8864272 1 Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP572644   loader:fastq load.py|options: readTypes=TBTT read1PairFiles=slc24a5 crispant with R848 S62 L005 R1 001.fastq.gz read2PairFiles=slc24a5 crispant with R848 S62 L005 R2 001.fastq.gz read3PairFiles=slc24a5 crispant with R848 S62 L005 I1 001.fastq.gz read4PairFiles=slc24a5 crispant with R848 S62 L005 I2 001.fastq.gz slc24a5_crispant_with_R848_S62_L005_I1_001.fastq.gz slc24a5_crispant_with_R848_S62_L005_I2_001.fastq.gz slc24a5_crispant_with_R848_S62_L005_R1_001.fastq.gz slc24a5_crispant_with_R848_S62_L005_R2_001.fastq.gz fastq fastq fastq fastq 67359016638.0 484597242.0 GSM8864272 r1 0:28 1:91 2:10 3:10 A:12101967291;C:10017190111;G:10977547337;T:10998758556;N:2885727 28 91 10 10 12101967291 10017190111 10977547337 10998758556 2885727 SRX28117244 SRS24473025 SRA2098862 Albert Einstein College of Medicine Albert Einstein College of Medicine                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2025-03-24 Larval Larval Blood Hematopoietic System
35487 35487 SRR32834033 SRX28117243 SRS24473024 SRP572644 PRJNA1241156 Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish GSE292726 Transcriptome Analysis Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.       mCherry cells rag1 crispant GSM8864271   tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|genotype:rag1 mosaic mutant|geo loc name:missing|collection date:missing mCherry cells rag1 crispant For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix Hematopoietic & Immune Cells The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used. Larvae were maintained in standard conditions at 28C cell type:Hematopoietic & Immune Cells|genotype:rag1 mosaic mutant GSM8864271 GSM8864271: mCherry cells rag1 crispant; Danio rerio; RNA Seq GSM8864271 r1 GSM8864271 1 Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP572644   loader:fastq load.py|options: readTypes=TBTT read1PairFiles=Rag1 crispant S63 L005 R1 001.fastq.gz read2PairFiles=Rag1 crispant S63 L005 R2 001.fastq.gz read3PairFiles=Rag1 crispant S63 L005 I1 001.fastq.gz read4PairFiles=Rag1 crispant S63 L005 I2 001.fastq.gz Rag1_crispant_S63_L005_I1_001.fastq.gz Rag1_crispant_S63_L005_I2_001.fastq.gz Rag1_crispant_S63_L005_R1_001.fastq.gz Rag1_crispant_S63_L005_R2_001.fastq.gz fastq fastq fastq fastq 40550115550.0 291727450.0 GSM8864271 r1 0:28 1:91 2:10 3:10 A:7262987235;C:6078752458;G:6639990009;T:6563701562;N:1766686 28 91 10 10 7262987235 6078752458 6639990009 6563701562 1766686 SRX28117243 SRS24473024 SRA2098862 Albert Einstein College of Medicine Albert Einstein College of Medicine                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2025-03-24 Larval Larval Blood Hematopoietic System
35488 35488 SRR32834034 SRX28117242 SRS24473022 SRP572644 PRJNA1241156 Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish GSE292726 Transcriptome Analysis Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.       mCherry cells slc24a5 crispant GSM8864270   tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|genotype:slc24a5 mosaic mutant|geo loc name:missing|collection date:missing mCherry cells slc24a5 crispant For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix Hematopoietic & Immune Cells The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used. Larvae were maintained in standard conditions at 28C cell type:Hematopoietic & Immune Cells|genotype:slc24a5 mosaic mutant GSM8864270 GSM8864270: mCherry cells slc24a5 crispant; Danio rerio; RNA Seq GSM8864270 r1 GSM8864270 1 Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP572644   loader:fastq load.py|options: readTypes=TBTT read1PairFiles=slc24a5 crispant S61 L005 R1 001.fastq.gz read2PairFiles=slc24a5 crispant S61 L005 R2 001.fastq.gz read3PairFiles=slc24a5 crispant S61 L005 I1 001.fastq.gz read4PairFiles=slc24a5 crispant S61 L005 I2 001.fastq.gz slc24a5_crispant_S61_L005_I1_001.fastq.gz slc24a5_crispant_S61_L005_I2_001.fastq.gz slc24a5_crispant_S61_L005_R1_001.fastq.gz slc24a5_crispant_S61_L005_R2_001.fastq.gz fastq fastq fastq fastq 53500554564.0 384896076.0 GSM8864270 r1 0:28 1:91 2:10 3:10 A:9607899809;C:8061049626;G:8772491787;T:8581787300;N:2314394 28 91 10 10 9607899809 8061049626 8772491787 8581787300 2314394 SRX28117242 SRS24473022 SRA2098862 Albert Einstein College of Medicine Albert Einstein College of Medicine                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2025-03-24 Larval Larval Blood Hematopoietic System
35489 35489 SRR32834035 SRX28117241 SRS24473017 SRP572644 PRJNA1241156 Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish GSE292726 Transcriptome Analysis Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.       mCherry cells runx1 homozygous mutants GSM8864269   tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|genotype:runx1 homozygous|geo loc name:missing|collection date:missing mCherry cells runx1 homozygous mutants For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix Hematopoietic & Immune Cells The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used. Larvae were maintained in standard conditions at 28C cell type:Hematopoietic & Immune Cells|genotype:runx1 homozygous GSM8864269 GSM8864269: mCherry cells runx1 homozygous mutants; Danio rerio; RNA Seq GSM8864269 r1 GSM8864269 1 Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP572644   loader:fastq load.py|options: readTypes=TBTT read1PairFiles=Runx1 Homz Mutants earlyHSPC trace 6 dpf S2 L002 R1 001.fastq.gz read2PairFiles=Runx1 Homz Mutants earlyHSPC trace 6 dpf S2 L002 R2 001.fastq.gz read3PairFiles=Runx1 Homz Mutants earlyHSPC trace 6 dpf S2 L002 I1 001.fastq.gz read4PairFiles=Runx1 Homz Mutants earlyHSPC trace 6 dpf S2 L002 I2 001.fastq.gz Runx1_Homz_Mutants_earlyHSPC_trace_6_dpf_S2_L002_I1_001.fastq.gz Runx1_Homz_Mutants_earlyHSPC_trace_6_dpf_S2_L002_I2_001.fastq.gz Runx1_Homz_Mutants_earlyHSPC_trace_6_dpf_S2_L002_R1_001.fastq.gz Runx1_Homz_Mutants_earlyHSPC_trace_6_dpf_S2_L002_R2_001.fastq.gz fastq fastq fastq fastq 27845512960.0 87017228.0 GSM8864269 r1 0:150 1:150 2:10 3:10 A:4012440512;C:2615250336;G:3042659166;T:3381797139;N:437047 150 150 10 10 4012440512 2615250336 3042659166 3381797139 437047 SRX28117241 SRS24473017 SRA2098862 Albert Einstein College of Medicine Albert Einstein College of Medicine                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2025-03-24 Larval Larval Blood Hematopoietic System
35490 35490 SRR32834036 SRX28117240 SRS24473018 SRP572644 PRJNA1241156 Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish GSE292726 Transcriptome Analysis Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.       mCherry cells sibling controls GSM8864268   tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|genotype:wild type or runx1 heterozygous|geo loc name:missing|collection date:missing mCherry cells sibling controls For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix Hematopoietic & Immune Cells The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used. Larvae were maintained in standard conditions at 28C cell type:Hematopoietic & Immune Cells|genotype:wild type or runx1 heterozygous GSM8864268 GSM8864268: mCherry cells sibling controls; Danio rerio; RNA Seq GSM8864268 r1 GSM8864268 1 Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP572644   loader:fastq load.py|options: readTypes=TBTT read1PairFiles=Sibling Control earlyHSPC trace 6 dpf S1 L002 R1 001.fastq.gz read2PairFiles=Sibling Control earlyHSPC trace 6 dpf S1 L002 R2 001.fastq.gz read3PairFiles=Sibling Control earlyHSPC trace 6 dpf S1 L002 I1 001.fastq.gz read4PairFiles=Sibling Control earlyHSPC trace 6 dpf S1 L002 I2 001.fastq.gz Sibling_Control_earlyHSPC_trace_6_dpf_S1_L002_I1_001.fastq.gz Sibling_Control_earlyHSPC_trace_6_dpf_S1_L002_I2_001.fastq.gz Sibling_Control_earlyHSPC_trace_6_dpf_S1_L002_R1_001.fastq.gz Sibling_Control_earlyHSPC_trace_6_dpf_S1_L002_R2_001.fastq.gz fastq fastq fastq fastq 24953253760.0 77978918.0 GSM8864268 r1 0:150 1:150 2:10 3:10 A:3390875336;C:2571521800;G:2871954356;T:2862416982;N:69226 150 150 10 10 3390875336 2571521800 2871954356 2862416982 69226 SRX28117240 SRS24473018 SRA2098862 Albert Einstein College of Medicine Albert Einstein College of Medicine                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2025-03-24 Larval Larval Blood Hematopoietic System
35491 35491 SRR32834037 SRX28117239 SRS24473015 SRP572644 PRJNA1241156 Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish GSE292726 Transcriptome Analysis Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.       mCherry cells late HSPCs 10 dpf GSM8864267   tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing mCherry cells late HSPCs 10 dpf For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix Hematopoietic & Immune Cells The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used. Larvae were maintained in standard conditions at 28C cell type:Hematopoietic & Immune Cells GSM8864267 GSM8864267: mCherry cells late HSPCs 10 dpf; Danio rerio; RNA Seq GSM8864267 r1 GSM8864267 1 Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP572644   loader:fastq load.py|options: readTypes=TBTT read1PairFiles=lateHSPC trace at 10dpf S1 L003 R1 001.fastq.gz read2PairFiles=lateHSPC trace at 10dpf S1 L003 R2 001.fastq.gz read3PairFiles=lateHSPC trace at 10dpf S1 L003 I1 001.fastq.gz read4PairFiles=lateHSPC trace at 10dpf S1 L003 I2 001.fastq.gz lateHSPC_trace_at_10dpf_S1_L003_I1_001.fastq.gz lateHSPC_trace_at_10dpf_S1_L003_I2_001.fastq.gz lateHSPC_trace_at_10dpf_S1_L003_R1_001.fastq.gz lateHSPC_trace_at_10dpf_S1_L003_R2_001.fastq.gz fastq fastq fastq fastq 49750537600.0 155470430.0 GSM8864267 r1 0:150 1:150 2:10 3:10 A:6695708919;C:5110107098;G:5648204020;T:5864962224;N:1582239 150 150 10 10 6695708919 5110107098 5648204020 5864962224 1582239 SRX28117239 SRS24473015 SRA2098862 Albert Einstein College of Medicine Albert Einstein College of Medicine                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2025-03-24 Larval Larval Blood Hematopoietic System
35492 35492 SRR32834038 SRX28117239 SRS24473015 SRP572644 PRJNA1241156 Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish GSE292726 Transcriptome Analysis Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.       mCherry cells late HSPCs 10 dpf GSM8864267   tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing mCherry cells late HSPCs 10 dpf For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix Hematopoietic & Immune Cells The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used. Larvae were maintained in standard conditions at 28C cell type:Hematopoietic & Immune Cells GSM8864267 GSM8864267: mCherry cells late HSPCs 10 dpf; Danio rerio; RNA Seq GSM8864267 r1 GSM8864267 1 Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP572644   loader:fastq load.py|options: readTypes=TBTT read1PairFiles=lateHSPC trace at 10dpf S18 L002 R1 001.fastq.gz read2PairFiles=lateHSPC trace at 10dpf S18 L002 R2 001.fastq.gz read3PairFiles=lateHSPC trace at 10dpf S18 L002 I1 001.fastq.gz read4PairFiles=lateHSPC trace at 10dpf S18 L002 I2 001.fastq.gz lateHSPC_trace_at_10dpf_S18_L002_I1_001.fastq.gz lateHSPC_trace_at_10dpf_S18_L002_I2_001.fastq.gz lateHSPC_trace_at_10dpf_S18_L002_R1_001.fastq.gz lateHSPC_trace_at_10dpf_S18_L002_R2_001.fastq.gz fastq fastq fastq fastq 3818546250.0 27670625.0 GSM8864267 r2 0:28 1:90 2:10 3:10 A:716133237;C:554493684;G:608989896;T:610460128;N:279305 28 90 10 10 716133237 554493684 608989896 610460128 279305 SRX28117239 SRS24473015 SRA2098862 Albert Einstein College of Medicine Albert Einstein College of Medicine                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2025-03-24 Larval Larval Blood Hematopoietic System
35493 35493 SRR32834039 SRX28117238 SRS24473019 SRP572644 PRJNA1241156 Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish GSE292726 Transcriptome Analysis Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.       mCherry cells late HSPCs 6 dpf GSM8864266   tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing mCherry cells late HSPCs 6 dpf For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix Hematopoietic & Immune Cells The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used. Larvae were maintained in standard conditions at 28C cell type:Hematopoietic & Immune Cells GSM8864266 GSM8864266: mCherry cells late HSPCs 6 dpf; Danio rerio; RNA Seq GSM8864266 r1 GSM8864266 1 Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP572644   loader:fastq load.py|options: readTypes=TBTT read1PairFiles=lateHSPC trace at 6dpf S17 L002 R1 001.fastq.gz read2PairFiles=lateHSPC trace at 6dpf S17 L002 R2 001.fastq.gz read3PairFiles=lateHSPC trace at 6dpf S17 L002 I1 001.fastq.gz read4PairFiles=lateHSPC trace at 6dpf S17 L002 I2 001.fastq.gz lateHSPC_trace_at_6dpf_S17_L002_I1_001.fastq.gz lateHSPC_trace_at_6dpf_S17_L002_I2_001.fastq.gz lateHSPC_trace_at_6dpf_S17_L002_R1_001.fastq.gz lateHSPC_trace_at_6dpf_S17_L002_R2_001.fastq.gz fastq fastq fastq fastq 12871712088.0 93273276.0 GSM8864266 r1 0:28 1:90 2:10 3:10 A:2421583617;C:1888963122;G:2078815965;T:2004213972;N:1018164 28 90 10 10 2421583617 1888963122 2078815965 2004213972 1018164 SRX28117238 SRS24473019 SRA2098862 Albert Einstein College of Medicine Albert Einstein College of Medicine                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2025-03-24 Larval Larval Blood Hematopoietic System
35494 35494 SRR32834040 SRX28117237 SRS24473014 SRP572644 PRJNA1241156 Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish GSE292726 Transcriptome Analysis Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.       mCherry cells late HSPCs 4 dpf GSM8864265   tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing mCherry cells late HSPCs 4 dpf For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix Hematopoietic & Immune Cells The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used. Larvae were maintained in standard conditions at 28C cell type:Hematopoietic & Immune Cells GSM8864265 GSM8864265: mCherry cells late HSPCs 4 dpf; Danio rerio; RNA Seq GSM8864265 r1 GSM8864265 1 Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP572644   loader:fastq load.py|options: readTypes=TBTT read1PairFiles=lateHSPC trace at 4dpf S16 L002 R1 001.fastq.gz read2PairFiles=lateHSPC trace at 4dpf S16 L002 R2 001.fastq.gz read3PairFiles=lateHSPC trace at 4dpf S16 L002 I1 001.fastq.gz read4PairFiles=lateHSPC trace at 4dpf S16 L002 I2 001.fastq.gz lateHSPC_trace_at_4dpf_S16_L002_I1_001.fastq.gz lateHSPC_trace_at_4dpf_S16_L002_I2_001.fastq.gz lateHSPC_trace_at_4dpf_S16_L002_R1_001.fastq.gz lateHSPC_trace_at_4dpf_S16_L002_R2_001.fastq.gz fastq fastq fastq fastq 11138275734.0 80712143.0 GSM8864265 r1 0:28 1:90 2:10 3:10 A:2022661838;C:1679042427;G:1720706851;T:1840857883;N:823871 28 90 10 10 2022661838 1679042427 1720706851 1840857883 823871 SRX28117237 SRS24473014 SRA2098862 Albert Einstein College of Medicine Albert Einstein College of Medicine                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2025-03-24 Larval Larval Blood Hematopoietic System
35495 35495 SRR32834041 SRX28117236 SRS24473016 SRP572644 PRJNA1241156 Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish GSE292726 Transcriptome Analysis Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.       mCherry cells mid HSPCs 10 dpf GSM8864264   tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing mCherry cells mid HSPCs 10 dpf For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix Hematopoietic & Immune Cells The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used. Larvae were maintained in standard conditions at 28C cell type:Hematopoietic & Immune Cells GSM8864264 GSM8864264: mCherry cells mid HSPCs 10 dpf; Danio rerio; RNA Seq GSM8864264 r1 GSM8864264 1 Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP572644   loader:fastq load.py|options: readTypes=TBTT read1PairFiles=midHSPC 10dpf S1 L001 R1 001.fastq.gz read2PairFiles=midHSPC 10dpf S1 L001 R2 001.fastq.gz read3PairFiles=midHSPC 10dpf S1 L001 I1 001.fastq.gz read4PairFiles=midHSPC 10dpf S1 L001 I2 001.fastq.gz midHSPC_10dpf_S1_L001_I1_001.fastq.gz midHSPC_10dpf_S1_L001_I2_001.fastq.gz midHSPC_10dpf_S1_L001_R1_001.fastq.gz midHSPC_10dpf_S1_L001_R2_001.fastq.gz fastq fastq fastq fastq 211217834240.0 660055732.0 GSM8864264 r1 0:150 1:150 2:10 3:10 A:28426769480;C:22300370613;G:24520861829;T:23758933345;N:1424533 150 150 10 10 28426769480 22300370613 24520861829 23758933345 1424533 SRX28117236 SRS24473016 SRA2098862 Albert Einstein College of Medicine Albert Einstein College of Medicine                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2025-03-24 Larval Larval Blood Hematopoietic System
35496 35496 SRR32834042 SRX28117235 SRS24473020 SRP572644 PRJNA1241156 Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish GSE292726 Transcriptome Analysis Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.       mCherry cells mid HSPCs 6 dpf GSM8864263   tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing mCherry cells mid HSPCs 6 dpf For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix Hematopoietic & Immune Cells The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used. Larvae were maintained in standard conditions at 28C cell type:Hematopoietic & Immune Cells GSM8864263 GSM8864263: mCherry cells mid HSPCs 6 dpf; Danio rerio; RNA Seq GSM8864263 r1 GSM8864263 1 Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP572644   loader:fastq load.py|options: readTypes=TBTT read1PairFiles=midHSPC 6dpf S1 L001 R1 001.fastq.gz read2PairFiles=midHSPC 6dpf S1 L001 R2 001.fastq.gz read3PairFiles=midHSPC 6dpf S1 L001 I1 001.fastq.gz read4PairFiles=midHSPC 6dpf S1 L001 I2 001.fastq.gz midHSPC_6dpf_S1_L001_I1_001.fastq.gz midHSPC_6dpf_S1_L001_I2_001.fastq.gz midHSPC_6dpf_S1_L001_R1_001.fastq.gz midHSPC_6dpf_S1_L001_R2_001.fastq.gz fastq fastq fastq fastq 241173414720.0 753666921.0 GSM8864263 r1                       SRX28117235 SRS24473020 SRA2098862 Albert Einstein College of Medicine Albert Einstein College of Medicine 1 0.94667   0.08748   0.83881   0.5015   150   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2025-03-24 Larval Larval Blood Hematopoietic System
35497 35497 SRR32834043 SRX28117234 SRS24473021 SRP572644 PRJNA1241156 Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish GSE292726 Transcriptome Analysis Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.       mCherry cells mid HSPCs 3 dpf GSM8864262   tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing mCherry cells mid HSPCs 3 dpf For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix Hematopoietic & Immune Cells The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used. Larvae were maintained in standard conditions at 28C cell type:Hematopoietic & Immune Cells GSM8864262 GSM8864262: mCherry cells mid HSPCs 3 dpf; Danio rerio; RNA Seq GSM8864262 r1 GSM8864262 1 Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP572644   loader:fastq load.py|options: readTypes=TBTT read1PairFiles=midHSPC 3dpf S6 L003 R1 001.fastq.gz read2PairFiles=midHSPC 3dpf S6 L003 R2 001.fastq.gz read3PairFiles=midHSPC 3dpf S6 L003 I1 001.fastq.gz read4PairFiles=midHSPC 3dpf S6 L003 I2 001.fastq.gz midHSPC_3dpf_S6_L003_I1_001.fastq.gz midHSPC_3dpf_S6_L003_I2_001.fastq.gz midHSPC_3dpf_S6_L003_R1_001.fastq.gz midHSPC_3dpf_S6_L003_R2_001.fastq.gz fastq fastq fastq fastq 71933359680.0 224791749.0 GSM8864262 r1 0:150 1:150 2:10 3:10 A:9519625855;C:6982221178;G:8366028895;T:7767873072;N:1083013350 150 150 10 10 9519625855 6982221178 8366028895 7767873072 1083013350 SRX28117234 SRS24473021 SRA2098862 Albert Einstein College of Medicine Albert Einstein College of Medicine 1 0.78368   0.08584   0.82144   0.50936   150   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2025-03-24 Larval Larval Blood Hematopoietic System
35498 35498 SRR32834044 SRX28117233 SRS24473012 SRP572644 PRJNA1241156 Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish GSE292726 Transcriptome Analysis Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.       mCherry cells early HSPCs 10 dpf GSM8864261   tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing mCherry cells early HSPCs 10 dpf For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix Hematopoietic & Immune Cells The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used. Larvae were maintained in standard conditions at 28C cell type:Hematopoietic & Immune Cells GSM8864261 GSM8864261: mCherry cells early HSPCs 10 dpf; Danio rerio; RNA Seq GSM8864261 r1 GSM8864261 1 Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP572644   loader:fastq load.py|options: readTypes=TBTT read1PairFiles=earlyHSPC 10dpf S1 L001 R1 001.fastq.gz read2PairFiles=earlyHSPC 10dpf S1 L001 R2 001.fastq.gz read3PairFiles=earlyHSPC 10dpf S1 L001 I1 001.fastq.gz read4PairFiles=earlyHSPC 10dpf S1 L001 I2 001.fastq.gz earlyHSPC_10dpf_S1_L001_I1_001.fastq.gz earlyHSPC_10dpf_S1_L001_I2_001.fastq.gz earlyHSPC_10dpf_S1_L001_R1_001.fastq.gz earlyHSPC_10dpf_S1_L001_R2_001.fastq.gz fastq fastq fastq fastq 267665197120.0 836453741.0 GSM8864261 r1                       SRX28117233 SRS24473012 SRA2098862 Albert Einstein College of Medicine Albert Einstein College of Medicine                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2025-03-24 Larval Larval Blood Hematopoietic System
35499 35499 SRR32834045 SRX28117232 SRS24473013 SRP572644 PRJNA1241156 Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish GSE292726 Transcriptome Analysis Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.       mCherry cells early HSPCs 6 dpf GSM8864260   tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing mCherry cells early HSPCs 6 dpf For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix Hematopoietic & Immune Cells The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used. Larvae were maintained in standard conditions at 28C cell type:Hematopoietic & Immune Cells GSM8864260 GSM8864260: mCherry cells early HSPCs 6 dpf; Danio rerio; RNA Seq GSM8864260 r1 GSM8864260 1 Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP572644   loader:fastq load.py|options: readTypes=TBTT read1PairFiles=earlyHSPC 6dpf S1 L001 R1 001.fastq.gz read2PairFiles=earlyHSPC 6dpf S1 L001 R2 001.fastq.gz read3PairFiles=earlyHSPC 6dpf S1 L001 I1 001.fastq.gz read4PairFiles=earlyHSPC 6dpf S1 L001 I2 001.fastq.gz earlyHSPC_6dpf_S1_L001_I1_001.fastq.gz earlyHSPC_6dpf_S1_L001_I2_001.fastq.gz earlyHSPC_6dpf_S1_L001_R1_001.fastq.gz earlyHSPC_6dpf_S1_L001_R2_001.fastq.gz fastq fastq fastq fastq 234759123200.0 733622260.0 GSM8864260 r1                       SRX28117232 SRS24473013 SRA2098862 Albert Einstein College of Medicine Albert Einstein College of Medicine                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2025-03-24 Larval Larval Blood Hematopoietic System
35500 35500 SRR32834046 SRX28117231 SRS24473011 SRP572644 PRJNA1241156 Single Cell Atlas Reveals Abundant Innate Lymphoid Cells in Larval Zebrafish GSE292726 Transcriptome Analysis Innate Lymphoid cells ILCs are a group of tissue resident lymphocytes that participate in immune defense and tissue homeostasis. The existence and ontogeny of ILCs during zebrafish embryonic development are not defined. During embryogenesis hematopoietic stem cells HSCs and HSC independent Progenitor Cells HPCs form contemporaneously and produce overlapping and distinct immune cell types. To delineate when ILCs emerge and if they originate exclusively from HSCs or HPCs we performed lineage tracing of the emerging hematopoietic system during larval development followed by single cell RNA sequencing of HSC and HPC progeny. To determine if the ILC like cells are derived from the definitive hematopoietic wave we did lineage tracing and scRNA seq experiment in runx1W84X mutants and illustrated that all ILC like clusters are Runx1 dependent. We confirmed that the transcriptionally detected larval ILC like cells are Rag independent and Il2rg dependent. Lastly embryonic ILCs are functional because they respond to an immune system stimulation with a viral mimic. The work provides fundamental knowledge on the early establishment of immune hierarchies and opens the zebrafish model to the exploration of ILC origination and function. Overall design: Experiment 1: for lineage tracing experiment HSPCs were labled with mCherry at 3 timepoints in development: either at 1 2 or 3 dpf. The differentiated progeny of labled HSPCs were sorted out from whole zebrafish using FACS at one day post labelling 6 dpf and 10 dpf. Experiment 2: for Runx1 mutants experiment early HSPCs 1dpf derived mCherry cells were isolated from sibling controls or homozygous runx1W84X mutants at 6 dpf from whole zebrafish. Experiment 3: for rag1/R848 experiment mCherry cells derived from early HSPCs 1dpf were isolated at 8 dpf from slc24a5 crispant controls rag1 crispants and from slc24a5 and rag1 crispants treated with R848 agonist.       mCherry cells early HSPCs 2 dpf GSM8864259   tissue:Hematopoietic & Immune Cells|cell type:Hematopoietic & Immune Cells|geo loc name:missing|collection date:missing mCherry cells early HSPCs 2 dpf For experiments 1 lineage tracing and 2 runx1 mutants CellRanger 7.0.1 was used. For experiment 3 slc24a5/rag1/R848 CellRanger 8.0.1 was used. The standard count function in Cell Ranger was used for all samples. Assembly: Danie rerio GRCz11 Supplementary files format and content: Matrix files CellRanger output filtered feature bc matrix Hematopoietic & Immune Cells The slc24a5 and rag1 crispants were treated with 25uM of Resiquimod R848 at 6 dpf Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used. Larvae were maintained in standard conditions at 28C cell type:Hematopoietic & Immune Cells GSM8864259 GSM8864259: mCherry cells early HSPCs 2 dpf; Danio rerio; RNA Seq GSM8864259 r1 GSM8864259 1 Zebrafish larvae were minced with a razor blade and collected into PBS. The suspension was then digested with Liberase for 15 min at 37C. FBS was used to inactivate the librase. Cells were filtered once before isolating via FACS. Libraries were prepared according to manufacturer's instructions of the kits. For experiments 1 lineage tracing & 2 runx1 mutants the Chromium Next GEM Single Cell three prime Kit v3.1 was used. For experiment 3 slc24a5/rag1/R848 the Chromium Next GEM Single Cell three prime Kit v4 was used.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP572644   loader:fastq load.py|options: readTypes=TBTT read1PairFiles=earlyHSPC 2dpf S5 L003 R1 001.fastq.gz read2PairFiles=earlyHSPC 2dpf S5 L003 R2 001.fastq.gz read3PairFiles=earlyHSPC 2dpf S5 L003 I1 001.fastq.gz read4PairFiles=earlyHSPC 2dpf S5 L003 I2 001.fastq.gz earlyHSPC_2dpf_S5_L003_I1_001.fastq.gz earlyHSPC_2dpf_S5_L003_I2_001.fastq.gz earlyHSPC_2dpf_S5_L003_R1_001.fastq.gz earlyHSPC_2dpf_S5_L003_R2_001.fastq.gz fastq fastq fastq fastq 80730897280.0 252284054.0 GSM8864259 r1 0:150 1:150 2:10 3:10 A:10564796609;C:7860706889;G:9394625294;T:8808848403;N:1213630905 150 150 10 10 10564796609 7860706889 9394625294 8808848403 1213630905 SRX28117231 SRS24473011 SRA2098862 Albert Einstein College of Medicine Albert Einstein College of Medicine                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2025-03-24 Multi-stage Multi-stage Blood Hematopoietic System
36249 36249 SRR34017907 SRX29213468 SRS25409913 SRP592701 PRJNA1278741 Single cell and in situ spatial analyses reveal the diversity of newly born hematopoietic stem cells and of their niches [scRNA Seq] GSE300039 Transcriptome Analysis Hematopoietic stem cells HSCs and more committed progenitors collectively referred to as HSPCs emerge from vessels during development via Endothelial to Hematopoietic Transition EHT. Recently using the zebrafish embryo we showed that two EHT cell types emerge from the dorsal aorta raising the question of their subsequent fate. To address this issue we established a complex pipeline based on single cell photoconversion and transgenic lines to characterize the abilities of EHT cell progenies to conquer hematopoietic organs and to obtain their transcriptomic profiles. We show that the two EHT cell types lead to partly differentially fated cells with significant differences in thymus colonization and T lymphoid lineage commitment. In addition we investigated implantation of HSPCs in niches with the support of HSPC signatures gata2b and cd34/podocalyxin retrieved from our single cell datasets. This revealed at unprecedented resolution the homing of HSPCs in niches of entire early larvae including the pronephros the sub aortic and caudal regions as well as the area contacting the supra intestinal artery. Our work provides new insights on fundamental aspects of HSPC fate acquisition from their emergence to their homing in specific niches. Overall design: Single cell transcriptomics analysis of newly born hematopoietic stem and progenitor cells. This dataset comprises progenies of cells photoconverted at 2dpf and sorted by FACS at 5dpf using the Tgkdrl:nls kikume transgenic line as well as sorted FACS hematopoietic cells from transgenic reporter lines namely from the Tgrunx1+23:eGFP and the outcross of the Tgcd41:eGFP and Tggata2b:RFP lines. Larvae were collected post dissection separating the rostral anterior and posterior region along a transversal section at the posterior limit of the elongated yolk and at the posterior limit of the swim bladder dissociation and sorting using a BD FACS AriaIII cell sorter. Progenies of photoconverted cells comprise progenies of single EHT photoconversion either EHT…   pubmed:40501392   5 dpf hematopoietic zebrafish cells session 2 GSM9052756   tissue:sorted hematopoietic cells|cell type:sorted hematopoietic cells|geo loc name:missing|collection date:missing 5 dpf hematopoietic zebrafish cells session 2 Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019 Assembly: zebrafish genome Lawson lab version 4.3.2. Supplementary files format and content: Tab separated value files sorted hematopoietic cells   Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al. 2018; Manoli and Driever 2012; Samsa et al. 2016. All steps were performed with cooled solutions 4°C and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly 5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine at a final concentration of 640 µg/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4°C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies Cat#: 12605 010 for 10 min on ice with gentle pipetting every 3 mins first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g before the TrypLE was removed and the cells were resuspended in 500 µl FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 μm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 µl of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples gating was done on SSC A vs. FSC A to collect cells then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher Cat#: D15106. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using …   cell type:sorted hematopoietic cells GSM9052756 GSM9052756: 5 dpf hematopoietic zebrafish cells session 2; Danio rerio; RNA Seq GSM9052756 r1 GSM9052756 1 Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al. 2018; Manoli and Driever 2012; Samsa et al. 2016. All steps were performed with cooled solutions 4°C and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly 5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine at a final concentration of 640 µg/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4°C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies Cat#: 12605 010 for 10 min on ice with gentle pipetting every 3 mins first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g before the TrypLE was removed and the cells were resuspended in 500 µl FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 μm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 µl of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples gating was done on SSC A vs. FSC A to collect cells then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher Cat#: D15106. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using …   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP592701     TORCQ_2023_S0_L001_R1_001.fastq.gz TORCQ_2023_S0_L001_R2_001.fastq.gz fastq fastq 9123251137.0 118483781.0 GSM9052756 r1 0:57 1:20 A:2003237489;C:1403878506;G:1540717140;T:1805684398;N:2369733604 57 20     2003237489 1403878506 1540717140 1805684398 2369733604 SRX29213468 SRS25409913 SRA2151098 Institut Pasteur Institut Pasteur                             illumina nextseq unknown random_priming unknown sc single_cell_plate marsseq   France 2025-06-17 Larval Larval Blood Hematopoietic System
36250 36250 SRR34017908 SRX29213468 SRS25409913 SRP592701 PRJNA1278741 Single cell and in situ spatial analyses reveal the diversity of newly born hematopoietic stem cells and of their niches [scRNA Seq] GSE300039 Transcriptome Analysis Hematopoietic stem cells HSCs and more committed progenitors collectively referred to as HSPCs emerge from vessels during development via Endothelial to Hematopoietic Transition EHT. Recently using the zebrafish embryo we showed that two EHT cell types emerge from the dorsal aorta raising the question of their subsequent fate. To address this issue we established a complex pipeline based on single cell photoconversion and transgenic lines to characterize the abilities of EHT cell progenies to conquer hematopoietic organs and to obtain their transcriptomic profiles. We show that the two EHT cell types lead to partly differentially fated cells with significant differences in thymus colonization and T lymphoid lineage commitment. In addition we investigated implantation of HSPCs in niches with the support of HSPC signatures gata2b and cd34/podocalyxin retrieved from our single cell datasets. This revealed at unprecedented resolution the homing of HSPCs in niches of entire early larvae including the pronephros the sub aortic and caudal regions as well as the area contacting the supra intestinal artery. Our work provides new insights on fundamental aspects of HSPC fate acquisition from their emergence to their homing in specific niches. Overall design: Single cell transcriptomics analysis of newly born hematopoietic stem and progenitor cells. This dataset comprises progenies of cells photoconverted at 2dpf and sorted by FACS at 5dpf using the Tgkdrl:nls kikume transgenic line as well as sorted FACS hematopoietic cells from transgenic reporter lines namely from the Tgrunx1+23:eGFP and the outcross of the Tgcd41:eGFP and Tggata2b:RFP lines. Larvae were collected post dissection separating the rostral anterior and posterior region along a transversal section at the posterior limit of the elongated yolk and at the posterior limit of the swim bladder dissociation and sorting using a BD FACS AriaIII cell sorter. Progenies of photoconverted cells comprise progenies of single EHT photoconversion either EHT…   pubmed:40501392   5 dpf hematopoietic zebrafish cells session 2 GSM9052756   tissue:sorted hematopoietic cells|cell type:sorted hematopoietic cells|geo loc name:missing|collection date:missing 5 dpf hematopoietic zebrafish cells session 2 Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019 Assembly: zebrafish genome Lawson lab version 4.3.2. Supplementary files format and content: Tab separated value files sorted hematopoietic cells   Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al. 2018; Manoli and Driever 2012; Samsa et al. 2016. All steps were performed with cooled solutions 4°C and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly 5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine at a final concentration of 640 µg/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4°C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies Cat#: 12605 010 for 10 min on ice with gentle pipetting every 3 mins first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g before the TrypLE was removed and the cells were resuspended in 500 µl FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 μm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 µl of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples gating was done on SSC A vs. FSC A to collect cells then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher Cat#: D15106. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using …   cell type:sorted hematopoietic cells GSM9052756 GSM9052756: 5 dpf hematopoietic zebrafish cells session 2; Danio rerio; RNA Seq GSM9052756 r1 GSM9052756 1 Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al. 2018; Manoli and Driever 2012; Samsa et al. 2016. All steps were performed with cooled solutions 4°C and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly 5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine at a final concentration of 640 µg/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4°C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies Cat#: 12605 010 for 10 min on ice with gentle pipetting every 3 mins first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g before the TrypLE was removed and the cells were resuspended in 500 µl FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 μm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 µl of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples gating was done on SSC A vs. FSC A to collect cells then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher Cat#: D15106. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using …   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP592701     TORCQ_2023_S0_L002_R1_001.fastq.gz TORCQ_2023_S0_L002_R2_001.fastq.gz fastq fastq 9249291128.0 120120664.0 GSM9052756 r2 0:57 1:20 A:2023532922;C:1427491871;G:1568162363;T:1827659977;N:2402443995 57 20     2023532922 1427491871 1568162363 1827659977 2402443995 SRX29213468 SRS25409913 SRA2151098 Institut Pasteur Institut Pasteur                             illumina nextseq unknown random_priming unknown sc single_cell_plate marsseq   France 2025-06-17 Larval Larval Blood Hematopoietic System
36251 36251 SRR34017909 SRX29213468 SRS25409913 SRP592701 PRJNA1278741 Single cell and in situ spatial analyses reveal the diversity of newly born hematopoietic stem cells and of their niches [scRNA Seq] GSE300039 Transcriptome Analysis Hematopoietic stem cells HSCs and more committed progenitors collectively referred to as HSPCs emerge from vessels during development via Endothelial to Hematopoietic Transition EHT. Recently using the zebrafish embryo we showed that two EHT cell types emerge from the dorsal aorta raising the question of their subsequent fate. To address this issue we established a complex pipeline based on single cell photoconversion and transgenic lines to characterize the abilities of EHT cell progenies to conquer hematopoietic organs and to obtain their transcriptomic profiles. We show that the two EHT cell types lead to partly differentially fated cells with significant differences in thymus colonization and T lymphoid lineage commitment. In addition we investigated implantation of HSPCs in niches with the support of HSPC signatures gata2b and cd34/podocalyxin retrieved from our single cell datasets. This revealed at unprecedented resolution the homing of HSPCs in niches of entire early larvae including the pronephros the sub aortic and caudal regions as well as the area contacting the supra intestinal artery. Our work provides new insights on fundamental aspects of HSPC fate acquisition from their emergence to their homing in specific niches. Overall design: Single cell transcriptomics analysis of newly born hematopoietic stem and progenitor cells. This dataset comprises progenies of cells photoconverted at 2dpf and sorted by FACS at 5dpf using the Tgkdrl:nls kikume transgenic line as well as sorted FACS hematopoietic cells from transgenic reporter lines namely from the Tgrunx1+23:eGFP and the outcross of the Tgcd41:eGFP and Tggata2b:RFP lines. Larvae were collected post dissection separating the rostral anterior and posterior region along a transversal section at the posterior limit of the elongated yolk and at the posterior limit of the swim bladder dissociation and sorting using a BD FACS AriaIII cell sorter. Progenies of photoconverted cells comprise progenies of single EHT photoconversion either EHT…   pubmed:40501392   5 dpf hematopoietic zebrafish cells session 2 GSM9052756   tissue:sorted hematopoietic cells|cell type:sorted hematopoietic cells|geo loc name:missing|collection date:missing 5 dpf hematopoietic zebrafish cells session 2 Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019 Assembly: zebrafish genome Lawson lab version 4.3.2. Supplementary files format and content: Tab separated value files sorted hematopoietic cells   Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al. 2018; Manoli and Driever 2012; Samsa et al. 2016. All steps were performed with cooled solutions 4°C and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly 5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine at a final concentration of 640 µg/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4°C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies Cat#: 12605 010 for 10 min on ice with gentle pipetting every 3 mins first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g before the TrypLE was removed and the cells were resuspended in 500 µl FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 μm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 µl of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples gating was done on SSC A vs. FSC A to collect cells then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher Cat#: D15106. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using …   cell type:sorted hematopoietic cells GSM9052756 GSM9052756: 5 dpf hematopoietic zebrafish cells session 2; Danio rerio; RNA Seq GSM9052756 r1 GSM9052756 1 Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al. 2018; Manoli and Driever 2012; Samsa et al. 2016. All steps were performed with cooled solutions 4°C and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly 5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine at a final concentration of 640 µg/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4°C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies Cat#: 12605 010 for 10 min on ice with gentle pipetting every 3 mins first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g before the TrypLE was removed and the cells were resuspended in 500 µl FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 μm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 µl of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples gating was done on SSC A vs. FSC A to collect cells then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher Cat#: D15106. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using …   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP592701     TORCQ_2023_S0_L003_R1_001.fastq.gz TORCQ_2023_S0_L003_R2_001.fastq.gz fastq fastq 9438695574.0 122580462.0 GSM9052756 r3 0:57 1:20 A:2061159862;C:1455510691;G:1599304279;T:1871072315;N:2451648427 57 20     2061159862 1455510691 1599304279 1871072315 2451648427 SRX29213468 SRS25409913 SRA2151098 Institut Pasteur Institut Pasteur                             illumina nextseq unknown random_priming unknown sc single_cell_plate marsseq   France 2025-06-17 Larval Larval Blood Hematopoietic System
36252 36252 SRR34017910 SRX29213468 SRS25409913 SRP592701 PRJNA1278741 Single cell and in situ spatial analyses reveal the diversity of newly born hematopoietic stem cells and of their niches [scRNA Seq] GSE300039 Transcriptome Analysis Hematopoietic stem cells HSCs and more committed progenitors collectively referred to as HSPCs emerge from vessels during development via Endothelial to Hematopoietic Transition EHT. Recently using the zebrafish embryo we showed that two EHT cell types emerge from the dorsal aorta raising the question of their subsequent fate. To address this issue we established a complex pipeline based on single cell photoconversion and transgenic lines to characterize the abilities of EHT cell progenies to conquer hematopoietic organs and to obtain their transcriptomic profiles. We show that the two EHT cell types lead to partly differentially fated cells with significant differences in thymus colonization and T lymphoid lineage commitment. In addition we investigated implantation of HSPCs in niches with the support of HSPC signatures gata2b and cd34/podocalyxin retrieved from our single cell datasets. This revealed at unprecedented resolution the homing of HSPCs in niches of entire early larvae including the pronephros the sub aortic and caudal regions as well as the area contacting the supra intestinal artery. Our work provides new insights on fundamental aspects of HSPC fate acquisition from their emergence to their homing in specific niches. Overall design: Single cell transcriptomics analysis of newly born hematopoietic stem and progenitor cells. This dataset comprises progenies of cells photoconverted at 2dpf and sorted by FACS at 5dpf using the Tgkdrl:nls kikume transgenic line as well as sorted FACS hematopoietic cells from transgenic reporter lines namely from the Tgrunx1+23:eGFP and the outcross of the Tgcd41:eGFP and Tggata2b:RFP lines. Larvae were collected post dissection separating the rostral anterior and posterior region along a transversal section at the posterior limit of the elongated yolk and at the posterior limit of the swim bladder dissociation and sorting using a BD FACS AriaIII cell sorter. Progenies of photoconverted cells comprise progenies of single EHT photoconversion either EHT…   pubmed:40501392   5 dpf hematopoietic zebrafish cells session 2 GSM9052756   tissue:sorted hematopoietic cells|cell type:sorted hematopoietic cells|geo loc name:missing|collection date:missing 5 dpf hematopoietic zebrafish cells session 2 Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019 Assembly: zebrafish genome Lawson lab version 4.3.2. Supplementary files format and content: Tab separated value files sorted hematopoietic cells   Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al. 2018; Manoli and Driever 2012; Samsa et al. 2016. All steps were performed with cooled solutions 4°C and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly 5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine at a final concentration of 640 µg/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4°C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies Cat#: 12605 010 for 10 min on ice with gentle pipetting every 3 mins first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g before the TrypLE was removed and the cells were resuspended in 500 µl FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 μm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 µl of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples gating was done on SSC A vs. FSC A to collect cells then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher Cat#: D15106. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using …   cell type:sorted hematopoietic cells GSM9052756 GSM9052756: 5 dpf hematopoietic zebrafish cells session 2; Danio rerio; RNA Seq GSM9052756 r1 GSM9052756 1 Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al. 2018; Manoli and Driever 2012; Samsa et al. 2016. All steps were performed with cooled solutions 4°C and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly 5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine at a final concentration of 640 µg/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4°C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies Cat#: 12605 010 for 10 min on ice with gentle pipetting every 3 mins first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g before the TrypLE was removed and the cells were resuspended in 500 µl FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 μm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 µl of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples gating was done on SSC A vs. FSC A to collect cells then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher Cat#: D15106. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using …   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP592701     TORCQ_2023_S0_L004_R1_001.fastq.gz TORCQ_2023_S0_L004_R2_001.fastq.gz fastq fastq 9409346870.0 122199310.0 GSM9052756 r4 0:57 1:20 A:2048111796;C:1451606983;G:1595602008;T:1870010070;N:2444016013 57 20     2048111796 1451606983 1595602008 1870010070 2444016013 SRX29213468 SRS25409913 SRA2151098 Institut Pasteur Institut Pasteur                             illumina nextseq unknown random_priming unknown sc single_cell_plate marsseq   France 2025-06-17 Larval Larval Blood Hematopoietic System
36253 36253 SRR34017905 SRX29213467 SRS25409912 SRP592701 PRJNA1278741 Single cell and in situ spatial analyses reveal the diversity of newly born hematopoietic stem cells and of their niches [scRNA Seq] GSE300039 Transcriptome Analysis Hematopoietic stem cells HSCs and more committed progenitors collectively referred to as HSPCs emerge from vessels during development via Endothelial to Hematopoietic Transition EHT. Recently using the zebrafish embryo we showed that two EHT cell types emerge from the dorsal aorta raising the question of their subsequent fate. To address this issue we established a complex pipeline based on single cell photoconversion and transgenic lines to characterize the abilities of EHT cell progenies to conquer hematopoietic organs and to obtain their transcriptomic profiles. We show that the two EHT cell types lead to partly differentially fated cells with significant differences in thymus colonization and T lymphoid lineage commitment. In addition we investigated implantation of HSPCs in niches with the support of HSPC signatures gata2b and cd34/podocalyxin retrieved from our single cell datasets. This revealed at unprecedented resolution the homing of HSPCs in niches of entire early larvae including the pronephros the sub aortic and caudal regions as well as the area contacting the supra intestinal artery. Our work provides new insights on fundamental aspects of HSPC fate acquisition from their emergence to their homing in specific niches. Overall design: Single cell transcriptomics analysis of newly born hematopoietic stem and progenitor cells. This dataset comprises progenies of cells photoconverted at 2dpf and sorted by FACS at 5dpf using the Tgkdrl:nls kikume transgenic line as well as sorted FACS hematopoietic cells from transgenic reporter lines namely from the Tgrunx1+23:eGFP and the outcross of the Tgcd41:eGFP and Tggata2b:RFP lines. Larvae were collected post dissection separating the rostral anterior and posterior region along a transversal section at the posterior limit of the elongated yolk and at the posterior limit of the swim bladder dissociation and sorting using a BD FACS AriaIII cell sorter. Progenies of photoconverted cells comprise progenies of single EHT photoconversion either EHT…   pubmed:40501392   5 dpf hematopoietic zebrafish cells session 1 GSM9052755   tissue:sorted hematopoietic cells|cell type:sorted hematopoietic cells|geo loc name:missing|collection date:missing 5 dpf hematopoietic zebrafish cells session 1 Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019 Assembly: zebrafish genome Lawson lab version 4.3.2. Supplementary files format and content: Tab separated value files sorted hematopoietic cells   Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al. 2018; Manoli and Driever 2012; Samsa et al. 2016. All steps were performed with cooled solutions 4°C and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly 5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine at a final concentration of 640 µg/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4°C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies Cat#: 12605 010 for 10 min on ice with gentle pipetting every 3 mins first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g before the TrypLE was removed and the cells were resuspended in 500 µl FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 μm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 µl of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples gating was done on SSC A vs. FSC A to collect cells then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher Cat#: D15106. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using …   cell type:sorted hematopoietic cells GSM9052755 GSM9052755: 5 dpf hematopoietic zebrafish cells session 1; Danio rerio; RNA Seq GSM9052755 r1 GSM9052755 1 Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al. 2018; Manoli and Driever 2012; Samsa et al. 2016. All steps were performed with cooled solutions 4°C and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly 5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine at a final concentration of 640 µg/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4°C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies Cat#: 12605 010 for 10 min on ice with gentle pipetting every 3 mins first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g before the TrypLE was removed and the cells were resuspended in 500 µl FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 μm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 µl of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples gating was done on SSC A vs. FSC A to collect cells then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher Cat#: D15106. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using …   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP592701     TORCQ_2021_S0_R1_001.fastq.gz TORCQ_2021_S0_R2_001.fastq.gz fastq fastq 45817068160.0 602856160.0 GSM9052755 r1 0:56 1:20 A:12324583812;C:8979463244;G:11486707902;T:13012728622;N:13584580 56 20     12324583812 8979463244 11486707902 13012728622 13584580 SRX29213467 SRS25409912 SRA2151098 Institut Pasteur Institut Pasteur                       B T sc-like readlen illumina nextseq unknown random_priming unknown sc single_cell_plate marsseq   France 2025-06-17 Larval Larval Blood Hematopoietic System
36254 36254 SRR34017906 SRX29213467 SRS25409912 SRP592701 PRJNA1278741 Single cell and in situ spatial analyses reveal the diversity of newly born hematopoietic stem cells and of their niches [scRNA Seq] GSE300039 Transcriptome Analysis Hematopoietic stem cells HSCs and more committed progenitors collectively referred to as HSPCs emerge from vessels during development via Endothelial to Hematopoietic Transition EHT. Recently using the zebrafish embryo we showed that two EHT cell types emerge from the dorsal aorta raising the question of their subsequent fate. To address this issue we established a complex pipeline based on single cell photoconversion and transgenic lines to characterize the abilities of EHT cell progenies to conquer hematopoietic organs and to obtain their transcriptomic profiles. We show that the two EHT cell types lead to partly differentially fated cells with significant differences in thymus colonization and T lymphoid lineage commitment. In addition we investigated implantation of HSPCs in niches with the support of HSPC signatures gata2b and cd34/podocalyxin retrieved from our single cell datasets. This revealed at unprecedented resolution the homing of HSPCs in niches of entire early larvae including the pronephros the sub aortic and caudal regions as well as the area contacting the supra intestinal artery. Our work provides new insights on fundamental aspects of HSPC fate acquisition from their emergence to their homing in specific niches. Overall design: Single cell transcriptomics analysis of newly born hematopoietic stem and progenitor cells. This dataset comprises progenies of cells photoconverted at 2dpf and sorted by FACS at 5dpf using the Tgkdrl:nls kikume transgenic line as well as sorted FACS hematopoietic cells from transgenic reporter lines namely from the Tgrunx1+23:eGFP and the outcross of the Tgcd41:eGFP and Tggata2b:RFP lines. Larvae were collected post dissection separating the rostral anterior and posterior region along a transversal section at the posterior limit of the elongated yolk and at the posterior limit of the swim bladder dissociation and sorting using a BD FACS AriaIII cell sorter. Progenies of photoconverted cells comprise progenies of single EHT photoconversion either EHT…   pubmed:40501392   5 dpf hematopoietic zebrafish cells session 1 GSM9052755   tissue:sorted hematopoietic cells|cell type:sorted hematopoietic cells|geo loc name:missing|collection date:missing 5 dpf hematopoietic zebrafish cells session 1 Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019 Assembly: zebrafish genome Lawson lab version 4.3.2. Supplementary files format and content: Tab separated value files sorted hematopoietic cells   Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al. 2018; Manoli and Driever 2012; Samsa et al. 2016. All steps were performed with cooled solutions 4°C and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly 5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine at a final concentration of 640 µg/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4°C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies Cat#: 12605 010 for 10 min on ice with gentle pipetting every 3 mins first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g before the TrypLE was removed and the cells were resuspended in 500 µl FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 μm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 µl of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples gating was done on SSC A vs. FSC A to collect cells then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher Cat#: D15106. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using …   cell type:sorted hematopoietic cells GSM9052755 GSM9052755: 5 dpf hematopoietic zebrafish cells session 1; Danio rerio; RNA Seq GSM9052755 r1 GSM9052755 1 Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al. 2018; Manoli and Driever 2012; Samsa et al. 2016. All steps were performed with cooled solutions 4°C and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly 5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine at a final concentration of 640 µg/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4°C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies Cat#: 12605 010 for 10 min on ice with gentle pipetting every 3 mins first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g before the TrypLE was removed and the cells were resuspended in 500 µl FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 μm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 µl of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples gating was done on SSC A vs. FSC A to collect cells then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher Cat#: D15106. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using …   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP592701     TORCQ_2021_S0_R1_001_small.fastq.gz TORCQ_2021_S0_R2_001_small.fastq.gz fastq fastq 190000.0 2500.0 GSM9052755 r2 0:56 1:20 A:50399;C:36081;G:47775;T:53618;N:2127 56 20     50399 36081 47775 53618 2127 SRX29213467 SRS25409912 SRA2151098 Institut Pasteur Institut Pasteur                       B T sc-like readlen illumina nextseq unknown random_priming unknown sc single_cell_plate marsseq   France 2025-06-17 Larval Larval Blood Hematopoietic System
37103 37103 SRR891512 SRX298192 SRS673882 SRP024369 PRJNA207719 Tissue specific transcriptome profiling of zebrafish PRJNA207719 Other Tissue specific transcriptome profiling of zebrafish.         Danio rerio blood   sex:missing|strain:wild type|tissue:blood|health state:normal|collection date:2013|geo loc name:India|biomaterial provider:CSIR Institute of Genomics and Integrative Biology|age:adult|BioSampleModel:Model organism or animal                 Tissue specific transcriptome of zebrafish Transcriptome of zebrafish Danio rerio blood zebrafish blood 1     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</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>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP024369     lane6_NoIndex_L006_R2_cat.fastq lane6_NoIndex_L006_R1_cat.fastq fastq fastq 2122070832.0 20804616.0 Transcriptome of zebrafish Danio rerio blood 0:51 1:51 A:508869849;C:550502747;G:580539251;T:481927903;N:231082 51 51     508869849 550502747 580539251 481927903 231082 SRX298192 SRS673882 SRA089174 CSIR-IGIB CSIR-Institute of Genomics and Integrative Biology CSIR-Institute of Genomics and Integrative Biology 2 0.78255 0.77496 0.03257 0.03239 0.75672 0.75542 0.44135 0.44382 51 51 B B biological fallback assumption illumina early_illumina unknown random_priming unknown bulk unknown unknown   India 2013-06-10 Adult Adult Blood Hematopoietic System
40807 40807 SRR3381847 SRX1704280 SRS1396343 SRP073272 PRJNA318414 Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults] GSE80260 Transcriptome Analysis Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos. parent bioproject:PRJNA318502 pubmed:27444789   Treated 3 blood GSM2122871   source name:whole blood cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol Treated 3 blood Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample. whole blood cortisol DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions. RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core. strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol GSM2122871 GSM2122871: Treated 3 blood; Danio rerio; RNA Seq GSM2122871   1 RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. GEO Accession:GSM2122871 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP073272     C8DY1ANXX_s6_1_GSLv3-7_38_SL139795.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_38_SL139795.fastq.gz fastq fastq 1349428600.0 13494286.0 GSM2122871 r1 0:50 1:50 A:391483366;C:283353944;G:288253777;T:386190051;N:147462 50 50     391483366 283353944 288253777 386190051 147462 SRX1704280 SRS1396343 SRA411416 GEO Molecular and Biomedical Sciences, University of Maine 2 0.88853 0.89204 0.22815 0.23941 0.73917 0.73979 0.53637 0.53893 50 50 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-13 Adult Adult Blood Hematopoietic System
40808 40808 SRR3381848 SRX1704280 SRS1396343 SRP073272 PRJNA318414 Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults] GSE80260 Transcriptome Analysis Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos. parent bioproject:PRJNA318502 pubmed:27444789   Treated 3 blood GSM2122871   source name:whole blood cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol Treated 3 blood Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample. whole blood cortisol DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions. RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core. strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol GSM2122871 GSM2122871: Treated 3 blood; Danio rerio; RNA Seq GSM2122871   1 RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. GEO Accession:GSM2122871 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP073272     C8BH2ANXX_s5_1_GSLv3-7_38_SL139795.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_38_SL139795.fastq.gz fastq fastq 1020366100.0 10203661.0 GSM2122871 r2 0:50 1:50 A:296023946;C:213173706;G:215342808;T:295806226;N:19414 50 50     296023946 213173706 215342808 295806226 19414 SRX1704280 SRS1396343 SRA411416 GEO Molecular and Biomedical Sciences, University of Maine 2 0.88792 0.89203 0.21382 0.24279 0.7652 0.7444 0.53618 0.54254 50 50 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-13 Adult Adult Blood Hematopoietic System
40809 40809 SRR3381849 SRX1704280 SRS1396343 SRP073272 PRJNA318414 Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults] GSE80260 Transcriptome Analysis Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos. parent bioproject:PRJNA318502 pubmed:27444789   Treated 3 blood GSM2122871   source name:whole blood cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol Treated 3 blood Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample. whole blood cortisol DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions. RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core. strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol GSM2122871 GSM2122871: Treated 3 blood; Danio rerio; RNA Seq GSM2122871   1 RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. GEO Accession:GSM2122871 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP073272     C8BH2ANXX_s6_1_GSLv3-7_38_SL139795.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_38_SL139795.fastq.gz fastq fastq 1008129000.0 10081290.0 GSM2122871 r3 0:50 1:50 A:292536545;C:210308039;G:212529262;T:292736486;N:18668 50 50     292536545 210308039 212529262 292736486 18668 SRX1704280 SRS1396343 SRA411416 GEO Molecular and Biomedical Sciences, University of Maine 2 0.88682 0.89249 0.21573 0.24321 0.7657 0.74456 0.53948 0.54456 50 50 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-13 Adult Adult Blood Hematopoietic System
40810 40810 SRR3381850 SRX1704280 SRS1396343 SRP073272 PRJNA318414 Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults] GSE80260 Transcriptome Analysis Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos. parent bioproject:PRJNA318502 pubmed:27444789   Treated 3 blood GSM2122871   source name:whole blood cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol Treated 3 blood Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample. whole blood cortisol DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions. RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core. strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol GSM2122871 GSM2122871: Treated 3 blood; Danio rerio; RNA Seq GSM2122871   1 RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. GEO Accession:GSM2122871 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP073272     C8DY1ANXX_s5_1_GSLv3-7_38_SL139795.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_38_SL139795.fastq.gz fastq fastq 1348814000.0 13488140.0 GSM2122871 r4 0:50 1:50 A:391186639;C:283404571;G:288274584;T:385756613;N:191593 50 50     391186639 283404571 288274584 385756613 191593 SRX1704280 SRS1396343 SRA411416 GEO Molecular and Biomedical Sciences, University of Maine 2 0.88673 0.89303 0.22875 0.24107 0.74276 0.74134 0.53585 0.54514 50 50 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-13 Adult Adult Blood Hematopoietic System
40811 40811 SRR3381843 SRX1704279 SRS1396344 SRP073272 PRJNA318414 Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults] GSE80260 Transcriptome Analysis Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos. parent bioproject:PRJNA318502 pubmed:27444789   Treated 2 blood GSM2122870   source name:whole blood cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol Treated 2 blood Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample. whole blood cortisol DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions. RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core. strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol GSM2122870 GSM2122870: Treated 2 blood; Danio rerio; RNA Seq GSM2122870   1 RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. GEO Accession:GSM2122870 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP073272     C8DY1ANXX_s6_1_GSLv3-7_37_SL139794.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_37_SL139794.fastq.gz fastq fastq 1251398700.0 12513987.0 GSM2122870 r1 0:50 1:50 A:383059535;C:243111832;G:248681985;T:376401618;N:143730 50 50     383059535 243111832 248681985 376401618 143730 SRX1704279 SRS1396344 SRA411416 GEO Molecular and Biomedical Sciences, University of Maine 2 0.86725 0.86597 0.35725 0.37228 0.74312 0.73961 0.53136 0.53663 50 50 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-13 Adult Adult Blood Hematopoietic System
40812 40812 SRR3381844 SRX1704279 SRS1396344 SRP073272 PRJNA318414 Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults] GSE80260 Transcriptome Analysis Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos. parent bioproject:PRJNA318502 pubmed:27444789   Treated 2 blood GSM2122870   source name:whole blood cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol Treated 2 blood Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample. whole blood cortisol DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions. RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core. strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol GSM2122870 GSM2122870: Treated 2 blood; Danio rerio; RNA Seq GSM2122870   1 RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. GEO Accession:GSM2122870 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP073272     C8BH2ANXX_s5_1_GSLv3-7_37_SL139794.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_37_SL139794.fastq.gz fastq fastq 959597100.0 9595971.0 GSM2122870 r2 0:50 1:50 A:294644349;C:184893976;G:188222172;T:291818696;N:17907 50 50     294644349 184893976 188222172 291818696 17907 SRX1704279 SRS1396344 SRA411416 GEO Molecular and Biomedical Sciences, University of Maine 2 0.86953 0.86626 0.33903 0.3765 0.77264 0.74432 0.53426 0.53782 50 50 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-13 Adult Adult Blood Hematopoietic System
40813 40813 SRR3381845 SRX1704279 SRS1396344 SRP073272 PRJNA318414 Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults] GSE80260 Transcriptome Analysis Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos. parent bioproject:PRJNA318502 pubmed:27444789   Treated 2 blood GSM2122870   source name:whole blood cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol Treated 2 blood Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample. whole blood cortisol DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions. RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core. strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol GSM2122870 GSM2122870: Treated 2 blood; Danio rerio; RNA Seq GSM2122870   1 RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. GEO Accession:GSM2122870 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP073272     C8DY1ANXX_s5_1_GSLv3-7_37_SL139794.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_37_SL139794.fastq.gz fastq fastq 1245250000.0 12452500.0 GSM2122870 r3 0:50 1:50 A:381219052;C:241987476;G:247543915;T:374295403;N:204154 50 50     381219052 241987476 247543915 374295403 204154 SRX1704279 SRS1396344 SRA411416 GEO Molecular and Biomedical Sciences, University of Maine 2 0.86789 0.86686 0.35484 0.37206 0.74119 0.73679 0.50299 0.53759 50 50 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-13 Adult Adult Blood Hematopoietic System
40814 40814 SRR3381846 SRX1704279 SRS1396344 SRP073272 PRJNA318414 Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults] GSE80260 Transcriptome Analysis Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos. parent bioproject:PRJNA318502 pubmed:27444789   Treated 2 blood GSM2122870   source name:whole blood cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol Treated 2 blood Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample. whole blood cortisol DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions. RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core. strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol GSM2122870 GSM2122870: Treated 2 blood; Danio rerio; RNA Seq GSM2122870   1 RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. GEO Accession:GSM2122870 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP073272     C8BH2ANXX_s6_1_GSLv3-7_37_SL139794.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_37_SL139794.fastq.gz fastq fastq 950337100.0 9503371.0 GSM2122870 r4 0:50 1:50 A:291821125;C:182753545;G:186179426;T:289565320;N:17684 50 50     291821125 182753545 186179426 289565320 17684 SRX1704279 SRS1396344 SRA411416 GEO Molecular and Biomedical Sciences, University of Maine 2 0.86635 0.86476 0.34245 0.3786 0.77309 0.74474 0.50694 0.53099 50 50 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-13 Adult Adult Blood Hematopoietic System
40815 40815 SRR3381839 SRX1704278 SRS1396345 SRP073272 PRJNA318414 Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults] GSE80260 Transcriptome Analysis Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos. parent bioproject:PRJNA318502 pubmed:27444789   Treated 1 blood GSM2122869   source name:whole blood cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol Treated 1 blood Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample. whole blood cortisol DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions. RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core. strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol GSM2122869 GSM2122869: Treated 1 blood; Danio rerio; RNA Seq GSM2122869   1 RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. GEO Accession:GSM2122869 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP073272     C8DY1ANXX_s5_1_GSLv3-7_36_SL139793.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_36_SL139793.fastq.gz fastq fastq 1067516000.0 10675160.0 GSM2122869 r1 0:50 1:50 A:289362409;C:244764167;G:247658920;T:285596522;N:133982 50 50     289362409 244764167 247658920 285596522 133982 SRX1704278 SRS1396345 SRA411416 GEO Molecular and Biomedical Sciences, University of Maine 2 0.90704 0.92219 0.1113 0.11316 0.73645 0.73746 0.52358 0.53128 50 50 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-13 Adult Adult Blood Hematopoietic System
40816 40816 SRR3381840 SRX1704278 SRS1396345 SRP073272 PRJNA318414 Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults] GSE80260 Transcriptome Analysis Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos. parent bioproject:PRJNA318502 pubmed:27444789   Treated 1 blood GSM2122869   source name:whole blood cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol Treated 1 blood Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample. whole blood cortisol DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions. RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core. strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol GSM2122869 GSM2122869: Treated 1 blood; Danio rerio; RNA Seq GSM2122869   1 RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. GEO Accession:GSM2122869 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP073272     C8BH2ANXX_s5_1_GSLv3-7_36_SL139793.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_36_SL139793.fastq.gz fastq fastq 802301400.0 8023014.0 GSM2122869 r2 0:50 1:50 A:216222361;C:183743858;G:183958773;T:218361744;N:14664 50 50     216222361 183743858 183958773 218361744 14664 SRX1704278 SRS1396345 SRA411416 GEO Molecular and Biomedical Sciences, University of Maine 2 0.90734 0.92073 0.10828 0.11414 0.75816 0.74156 0.52518 0.53162 50 50 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-13 Adult Adult Blood Hematopoietic System
40817 40817 SRR3381841 SRX1704278 SRS1396345 SRP073272 PRJNA318414 Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults] GSE80260 Transcriptome Analysis Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos. parent bioproject:PRJNA318502 pubmed:27444789   Treated 1 blood GSM2122869   source name:whole blood cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol Treated 1 blood Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample. whole blood cortisol DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions. RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core. strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol GSM2122869 GSM2122869: Treated 1 blood; Danio rerio; RNA Seq GSM2122869   1 RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. GEO Accession:GSM2122869 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP073272     C8DY1ANXX_s6_1_GSLv3-7_36_SL139793.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_36_SL139793.fastq.gz fastq fastq 1068410400.0 10684104.0 GSM2122869 r3 0:50 1:50 A:289709397;C:244889156;G:247758297;T:285941886;N:111664 50 50     289709397 244889156 247758297 285941886 111664 SRX1704278 SRS1396345 SRA411416 GEO Molecular and Biomedical Sciences, University of Maine 2 0.90673 0.9217 0.11124 0.11262 0.73779 0.73819 0.52628 0.53419 50 50 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-13 Adult Adult Blood Hematopoietic System
40818 40818 SRR3381842 SRX1704278 SRS1396345 SRP073272 PRJNA318414 Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults] GSE80260 Transcriptome Analysis Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos. parent bioproject:PRJNA318502 pubmed:27444789   Treated 1 blood GSM2122869   source name:whole blood cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol Treated 1 blood Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample. whole blood cortisol DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions. RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core. strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol GSM2122869 GSM2122869: Treated 1 blood; Danio rerio; RNA Seq GSM2122869   1 RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. GEO Accession:GSM2122869 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP073272     C8BH2ANXX_s6_1_GSLv3-7_36_SL139793.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_36_SL139793.fastq.gz fastq fastq 792180400.0 7921804.0 GSM2122869 r4 0:50 1:50 A:213515752;C:181199374;G:181507201;T:215943851;N:14222 50 50     213515752 181199374 181507201 215943851 14222 SRX1704278 SRS1396345 SRA411416 GEO Molecular and Biomedical Sciences, University of Maine 2 0.90574 0.92099 0.11022 0.11558 0.75773 0.74158 0.52565 0.52697 50 50 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-13 Adult Adult Blood Hematopoietic System
40819 40819 SRR3381835 SRX1704277 SRS1396346 SRP073272 PRJNA318414 Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults] GSE80260 Transcriptome Analysis Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos. parent bioproject:PRJNA318502 pubmed:27444789   Control 3 blood GSM2122868   source name:whole blood DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO Control 3 blood Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample. whole blood DMSO control DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions. RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core. strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO GSM2122868 GSM2122868: Control 3 blood; Danio rerio; RNA Seq GSM2122868   1 RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. GEO Accession:GSM2122868 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP073272     C8BH2ANXX_s6_1_GSLv3-7_35_SL139792.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_35_SL139792.fastq.gz fastq fastq 1006437300.0 10064373.0 GSM2122868 r1 0:50 1:50 A:270736589;C:231073543;G:230348781;T:274259695;N:18692 50 50     270736589 231073543 230348781 274259695 18692 SRX1704277 SRS1396346 SRA411416 GEO Molecular and Biomedical Sciences, University of Maine 2 0.89576 0.91552 0.11015 0.11108 0.77108 0.75708 0.52238 0.55295 50 50 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-13 Adult Adult Blood Hematopoietic System
40820 40820 SRR3381836 SRX1704277 SRS1396346 SRP073272 PRJNA318414 Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults] GSE80260 Transcriptome Analysis Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos. parent bioproject:PRJNA318502 pubmed:27444789   Control 3 blood GSM2122868   source name:whole blood DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO Control 3 blood Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample. whole blood DMSO control DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions. RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core. strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO GSM2122868 GSM2122868: Control 3 blood; Danio rerio; RNA Seq GSM2122868   1 RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. GEO Accession:GSM2122868 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP073272     C8BH2ANXX_s5_1_GSLv3-7_35_SL139792.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_35_SL139792.fastq.gz fastq fastq 1019872300.0 10198723.0 GSM2122868 r2 0:50 1:50 A:274310405;C:234397316;G:233653220;T:277492635;N:18724 50 50     274310405 234397316 233653220 277492635 18724 SRX1704277 SRS1396346 SRA411416 GEO Molecular and Biomedical Sciences, University of Maine 2 0.89872 0.91671 0.10908 0.10998 0.76848 0.7559 0.55678 0.52913 50 50 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-13 Adult Adult Blood Hematopoietic System
40821 40821 SRR3381837 SRX1704277 SRS1396346 SRP073272 PRJNA318414 Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults] GSE80260 Transcriptome Analysis Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos. parent bioproject:PRJNA318502 pubmed:27444789   Control 3 blood GSM2122868   source name:whole blood DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO Control 3 blood Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample. whole blood DMSO control DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions. RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core. strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO GSM2122868 GSM2122868: Control 3 blood; Danio rerio; RNA Seq GSM2122868   1 RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. GEO Accession:GSM2122868 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP073272     C8DY1ANXX_s6_1_GSLv3-7_35_SL139792.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_35_SL139792.fastq.gz fastq fastq 1350419100.0 13504191.0 GSM2122868 r3 0:50 1:50 A:365416324;C:310498635;G:312632921;T:361739733;N:131487 50 50     365416324 310498635 312632921 361739733 131487 SRX1704277 SRS1396346 SRA411416 GEO Molecular and Biomedical Sciences, University of Maine 2 0.89828 0.91602 0.11147 0.11073 0.74941 0.75053 0.54012 0.53979 50 50 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-13 Adult Adult Blood Hematopoietic System
40822 40822 SRR3381838 SRX1704277 SRS1396346 SRP073272 PRJNA318414 Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults] GSE80260 Transcriptome Analysis Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos. parent bioproject:PRJNA318502 pubmed:27444789   Control 3 blood GSM2122868   source name:whole blood DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO Control 3 blood Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample. whole blood DMSO control DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions. RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core. strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO GSM2122868 GSM2122868: Control 3 blood; Danio rerio; RNA Seq GSM2122868   1 RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. GEO Accession:GSM2122868 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP073272     C8DY1ANXX_s5_1_GSLv3-7_35_SL139792.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_35_SL139792.fastq.gz fastq fastq 1352817900.0 13528179.0 GSM2122868 r4 0:50 1:50 A:366001448;C:311109301;G:313269573;T:362247619;N:189959 50 50     366001448 311109301 313269573 362247619 189959 SRX1704277 SRS1396346 SRA411416 GEO Molecular and Biomedical Sciences, University of Maine 2 0.89762 0.91702 0.11094 0.1109 0.74864 0.7498 0.53153 0.55731 50 50 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-13 Adult Adult Blood Hematopoietic System
40823 40823 SRR3381831 SRX1704276 SRS1396347 SRP073272 PRJNA318414 Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults] GSE80260 Transcriptome Analysis Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos. parent bioproject:PRJNA318502 pubmed:27444789   Control 2 blood GSM2122867   source name:whole blood DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO Control 2 blood Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample. whole blood DMSO control DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions. RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core. strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO GSM2122867 GSM2122867: Control 2 blood; Danio rerio; RNA Seq GSM2122867   1 RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. GEO Accession:GSM2122867 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP073272     C8DY1ANXX_s5_1_GSLv3-7_34_SL139791.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_34_SL139791.fastq.gz fastq fastq 1320276500.0 13202765.0 GSM2122867 r1 0:50 1:50 A:347340148;C:314346533;G:315984111;T:342435896;N:169812 50 50     347340148 314346533 315984111 342435896 169812 SRX1704276 SRS1396347 SRA411416 GEO Molecular and Biomedical Sciences, University of Maine 2 0.92673 0.93522 0.1474 0.1486 0.77695 0.77822 0.5491 0.55404 50 50 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-13 Adult Adult Blood Hematopoietic System
40824 40824 SRR3381832 SRX1704276 SRS1396347 SRP073272 PRJNA318414 Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults] GSE80260 Transcriptome Analysis Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos. parent bioproject:PRJNA318502 pubmed:27444789   Control 2 blood GSM2122867   source name:whole blood DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO Control 2 blood Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample. whole blood DMSO control DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions. RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core. strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO GSM2122867 GSM2122867: Control 2 blood; Danio rerio; RNA Seq GSM2122867   1 RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. GEO Accession:GSM2122867 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP073272     C8BH2ANXX_s6_1_GSLv3-7_34_SL139791.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_34_SL139791.fastq.gz fastq fastq 980312400.0 9803124.0 GSM2122867 r2 0:50 1:50 A:256051139;C:233456025;G:232307447;T:258480444;N:17345 50 50     256051139 233456025 232307447 258480444 17345 SRX1704276 SRS1396347 SRA411416 GEO Molecular and Biomedical Sciences, University of Maine 2 0.92686 0.9359 0.1445 0.14733 0.79537 0.78244 0.55823 0.5607 50 50 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-13 Adult Adult Blood Hematopoietic System
40825 40825 SRR3381833 SRX1704276 SRS1396347 SRP073272 PRJNA318414 Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults] GSE80260 Transcriptome Analysis Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos. parent bioproject:PRJNA318502 pubmed:27444789   Control 2 blood GSM2122867   source name:whole blood DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO Control 2 blood Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample. whole blood DMSO control DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions. RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core. strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO GSM2122867 GSM2122867: Control 2 blood; Danio rerio; RNA Seq GSM2122867   1 RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. GEO Accession:GSM2122867 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP073272     C8BH2ANXX_s5_1_GSLv3-7_34_SL139791.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_34_SL139791.fastq.gz fastq fastq 996477700.0 9964777.0 GSM2122867 r3 0:50 1:50 A:260257795;C:237526121;G:236299803;T:262375630;N:18351 50 50     260257795 237526121 236299803 262375630 18351 SRX1704276 SRS1396347 SRA411416 GEO Molecular and Biomedical Sciences, University of Maine 2 0.9292 0.93713 0.143 0.14889 0.79531 0.7834 0.55615 0.55279 50 50 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-13 Adult Adult Blood Hematopoietic System
40826 40826 SRR3381834 SRX1704276 SRS1396347 SRP073272 PRJNA318414 Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults] GSE80260 Transcriptome Analysis Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos. parent bioproject:PRJNA318502 pubmed:27444789   Control 2 blood GSM2122867   source name:whole blood DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO Control 2 blood Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample. whole blood DMSO control DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions. RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core. strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO GSM2122867 GSM2122867: Control 2 blood; Danio rerio; RNA Seq GSM2122867   1 RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. GEO Accession:GSM2122867 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP073272     C8DY1ANXX_s6_1_GSLv3-7_34_SL139791.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_34_SL139791.fastq.gz fastq fastq 1319184300.0 13191843.0 GSM2122867 r4 0:50 1:50 A:347098468;C:314043165;G:315610117;T:342302442;N:130108 50 50     347098468 314043165 315610117 342302442 130108 SRX1704276 SRS1396347 SRA411416 GEO Molecular and Biomedical Sciences, University of Maine 2 0.92671 0.93595 0.14826 0.14877 0.77792 0.77873 0.55524 0.5557 50 50 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-13 Adult Adult Blood Hematopoietic System
40827 40827 SRR3381825 SRX1704275 SRS1396348 SRP073272 PRJNA318414 Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults] GSE80260 Transcriptome Analysis Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos. parent bioproject:PRJNA318502 pubmed:27444789   Control 1 blood GSM2122866   source name:whole blood DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO Control 1 blood Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample. whole blood DMSO control DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions. RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core. strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO GSM2122866 GSM2122866: Control 1 blood; Danio rerio; RNA Seq GSM2122866   1 RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. GEO Accession:GSM2122866 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP073272     C8BH2ANXX_s6_1_GSLv3-7_33_SL139790.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_33_SL139790.fastq.gz fastq fastq 692276000.0 6922760.0 GSM2122866 r1 0:50 1:50 A:191405813;C:153586292;G:152965257;T:194306049;N:12589 50 50     191405813 153586292 152965257 194306049 12589 SRX1704275 SRS1396348 SRA411416 GEO Molecular and Biomedical Sciences, University of Maine 2 0.9083 0.91142 0.16578 0.17743 0.75789 0.74221 0.55181 0.54476 50 50 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-13 Adult Adult Blood Hematopoietic System
40828 40828 SRR3381826 SRX1704275 SRS1396348 SRP073272 PRJNA318414 Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults] GSE80260 Transcriptome Analysis Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos. parent bioproject:PRJNA318502 pubmed:27444789   Control 1 blood GSM2122866   source name:whole blood DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO Control 1 blood Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample. whole blood DMSO control DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions. RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core. strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO GSM2122866 GSM2122866: Control 1 blood; Danio rerio; RNA Seq GSM2122866   1 RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. GEO Accession:GSM2122866 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP073272     C8DY1ANXX_s5_1_GSLv3-7_33_SL139790.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_33_SL139790.fastq.gz fastq fastq 911479300.0 9114793.0 GSM2122866 r2 0:50 1:50 A:253240601;C:202627238;G:203390297;T:252105631;N:115533 50 50     253240601 202627238 203390297 252105631 115533 SRX1704275 SRS1396348 SRA411416 GEO Molecular and Biomedical Sciences, University of Maine 2 0.90729 0.91334 0.17307 0.1777 0.73316 0.73419 0.55981 0.56826 50 50 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-13 Adult Adult Blood Hematopoietic System
40829 40829 SRR3381827 SRX1704275 SRS1396348 SRP073272 PRJNA318414 Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults] GSE80260 Transcriptome Analysis Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration heightened basal expression of pro inflammatory genes and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0 2 and 4dpa 3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos. parent bioproject:PRJNA318502 pubmed:27444789   Control 1 blood GSM2122866   source name:whole blood DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO Control 1 blood Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al. 2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey 2011 and Bowtie 1.1.2 Langmead et al. 2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al. 2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample. whole blood DMSO control DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development and then maintained to 4.5 month under normal conditions. RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core. strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO GSM2122866 GSM2122866: Control 1 blood; Danio rerio; RNA Seq GSM2122866   1 RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries. GEO Accession:GSM2122866 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP073272     C8DY1ANXX_s6_1_GSLv3-7_33_SL139790.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_33_SL139790.fastq.gz fastq fastq 910041600.0 9100416.0 GSM2122866 r3 0:50 1:50 A:252924440;C:202200821;G:202972517;T:251856107;N:87715 50 50     252924440 202200821 202972517 251856107 87715 SRX1704275 SRS1396348 SRA411416 GEO Molecular and Biomedical Sciences, University of Maine 2 0.90819 0.91345 0.17288 0.17678 0.73582 0.73448 0.55482 0.56579 50 50 B B biological fallback assumption illumina hiseq_era unknown poly_a trueseq bulk unknown unknown   United States 2016-04-13 Adult Adult Blood Hematopoietic 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");;