RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

268 rows where experiment.library_strategy = "RNA-Seq", technology = "unknown" and tissue_curation_coarse = "Hematopoietic System"

✎ View and edit SQL

This data as json, CSV (advanced)

experiment.library_selection 7

devstage_curation 5

devstage_curation_coarse 4

tissue_curation 3

experiment.platform 2

experiment.library_layout 2

tissue_curation_coarse 1

  • Hematopoietic System · 268 ✖

technology 1

  • unknown · 268 ✖

experiment.library_strategy 1

  • RNA-Seq · 268 ✖

experiment.library_source 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
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
25304 25304 SRR25793376 SRX21515638 SRS18742880 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.       RNA seq Erythrocytes miR 144 adult miR 144 adult   isolate:miR 144 mutant|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal                 Quant seq Erythrocytes miR 144 mutant Danio rerio ADULT replicate 1 144 1 adult blood 144 1 adult blood Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457465     DC-144AL1_S10.fastq fastq 781435052.0 17368946.0 DC 144AL1 S10.fastq 0:44.99 A:207445570;C:148430622;G:177122903;T:245179579;N:3256378 44       207445570 148430622 177122903 245179579 3256378 SRX21515638 SRS18742880 SRA1701831 University of East Anglia|Biological Sciences University of East Anglia 1 0.8759   0.28126   0.95051   0.47905   22   B   usable mapping rate illumina novaseq_era 3prime poly_a lexogen bulk unknown unknown   United Kingdom 2023-08-30 Adult Adult Blood Hematopoietic System
25305 25305 SRR25793377 SRX21515637 SRS18742882 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.       RNA seq Erythrocytes Wild type adult WT adult   isolate:Wildtype|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal                 Quant seq Erythrocytes Wild type Danio rerio ADULT replicate 3 WT3 adult blood WT3 adult blood Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457465     DC-WTA3_S6.fastq fastq 601997398.0 17290043.0 DC WTA3 S6.fastq 0:34.82 A:136034449;C:142779447;G:177204517;T:134955264;N:11023721 34       136034449 142779447 177204517 134955264 11023721 SRX21515637 SRS18742882 SRA1701831 University of East Anglia|Biological Sciences University of East Anglia 1 0.32909   0.08525   0.95288   0.60214   22   B   usable mapping rate illumina novaseq_era 3prime poly_a lexogen bulk unknown unknown   United Kingdom 2023-08-30 Adult Adult Blood Hematopoietic System
25306 25306 SRR25793378 SRX21515636 SRS18742882 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.       RNA seq Erythrocytes Wild type adult WT adult   isolate:Wildtype|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal                 Quant seq Erythrocytes Wild type Danio rerio ADULT replicate 2 WT2 adult blood WT2 adult blood Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457465     DC-WTA2_S5.fastq fastq 669871903.0 17381581.0 DC WTA2 S5.fastq 0:38.54 A:169704437;C:140964096;G:160484620;T:189596855;N:9121895 38       169704437 140964096 160484620 189596855 9121895 SRX21515636 SRS18742882 SRA1701831 University of East Anglia|Biological Sciences University of East Anglia 1 0.69865   0.19099   0.93432   0.47502   68   B   usable mapping rate illumina novaseq_era 3prime poly_a lexogen bulk unknown unknown   United Kingdom 2023-08-30 Adult Adult Blood Hematopoietic System
25307 25307 SRR25793379 SRX21515635 SRS18742882 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.       RNA seq Erythrocytes Wild type adult WT adult   isolate:Wildtype|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal                 Quant seq Erythrocytes Wild type Danio rerio ADULT replicate 1 WT1 adult blood WT1 adult blood Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457465     DC-WTA1_S4.fastq fastq 824193699.0 17465379.0 DC WTA1 S4.fastq 0:47.19 A:209553199;C:169966117;G:194322860;T:244145525;N:6205998 47       209553199 169966117 194322860 244145525 6205998 SRX21515635 SRS18742882 SRA1701831 University of East Anglia|Biological Sciences University of East Anglia 1 0.76241   0.25975   0.94619   0.50211   66   B   usable mapping rate illumina novaseq_era 3prime poly_a lexogen bulk unknown unknown   United Kingdom 2023-08-30 Adult Adult Blood Hematopoietic System
25308 25308 SRR25793380 SRX21515634 SRS18742881 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.       RNA seq Erythrocytes miR 144 embryo miR 144 embryo   isolate:miR 144 mutant|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal                 Quant seq Erythrocytes miR 144 mutant Danio rerio 2 dpf replicate 3 144 3 embryo blood 144 3 embryo blood Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457465     DC-144EL3_S18.fastq fastq 687309797.0 17039739.0 DC 144EL3 S18.fastq 0:40.34 A:159186558;C:130452893;G:155820002;T:181676510;N:60173834 40       159186558 130452893 155820002 181676510 60173834 SRX21515634 SRS18742881 SRA1701831 University of East Anglia|Biological Sciences University of East Anglia 1 0.52966   0.16941   0.97615   0.58418   61   B   usable mapping rate illumina novaseq_era 3prime poly_a lexogen bulk unknown unknown   United Kingdom 2023-08-30 Hatching Embryo Blood Hematopoietic System
25309 25309 SRR25793381 SRX21515633 SRS18742881 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.       RNA seq Erythrocytes miR 144 embryo miR 144 embryo   isolate:miR 144 mutant|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal                 Quant seq Erythrocytes miR 144 mutant Danio rerio 2 dpf replicate 2 144 2 embryo blood 144 2 embryo blood Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457465     DC-144EL2_S17.fastq fastq 495318731.0 14459195.0 DC 144EL2 S17.fastq 0:34.26 A:110392869;C:106378418;G:128881687;T:107956679;N:41709078 34       110392869 106378418 128881687 107956679 41709078 SRX21515633 SRS18742881 SRA1701831 University of East Anglia|Biological Sciences University of East Anglia 1 0.32147   0.04496   0.97569   0.58512   31   B   usable mapping rate illumina novaseq_era 3prime poly_a lexogen bulk unknown unknown   United Kingdom 2023-08-30 Hatching Embryo Blood Hematopoietic System
25310 25310 SRR25793382 SRX21515632 SRS18742881 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.       RNA seq Erythrocytes miR 144 embryo miR 144 embryo   isolate:miR 144 mutant|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal                 Quant seq Erythrocytes miR 144 mutant Danio rerio 2 dpf replicate 1 144 1 embryo blood 144 1 embryo blood Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457465     DC-144EL1_S16.fastq fastq 974854100.0 20079553.0 DC 144EL1 S16.fastq 0:48.55 A:233861010;C:192987350;G:215192262;T:269960344;N:62853134 48       233861010 192987350 215192262 269960344 62853134 SRX21515632 SRS18742881 SRA1701831 University of East Anglia|Biological Sciences University of East Anglia 1 0.77953   0.18084   0.90905   0.74157   75   B   usable mapping rate illumina novaseq_era 3prime poly_a lexogen bulk unknown unknown   United Kingdom 2023-08-30 Hatching Embryo Blood Hematopoietic System
25311 25311 SRR25793383 SRX21515631 SRS18742879 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.       RNA seq Erythrocytes Wild type embryo WT embryo   isolate:Wildtype|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal                 Quant seq Erythrocytes Wild type Danio rerio 2 dpf replicate 3 WT3 embryo blood WT3 embryo blood Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457465     DC-WTE3_S15.fastq fastq 657139116.0 15618072.0 DC WTE3 S15.fastq 0:42.08 A:154495614;C:122942896;G:147719345;T:179403193;N:52578068 42       154495614 122942896 147719345 179403193 52578068 SRX21515631 SRS18742879 SRA1701831 University of East Anglia|Biological Sciences University of East Anglia 1 0.56358   0.19381   0.96757   0.6115   76   B   usable mapping rate illumina novaseq_era 3prime poly_a lexogen bulk unknown unknown   United Kingdom 2023-08-30 Hatching Embryo Blood Hematopoietic System
25312 25312 SRR25793384 SRX21515630 SRS18742880 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.       RNA seq Erythrocytes miR 144 adult miR 144 adult   isolate:miR 144 mutant|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal                 Quant seq Erythrocytes miR 144 mutant Danio rerio ADULT replicate 3 144 3 adult blood 144 3 adult blood Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457465     DC-144AL3_S12.fastq fastq 498938612.0 14861511.0 DC 144AL3 S12.fastq 0:33.57 A:137243823;C:96735877;G:109220779;T:152042235;N:3695898 33       137243823 96735877 109220779 152042235 3695898 SRX21515630 SRS18742880 SRA1701831 University of East Anglia|Biological Sciences University of East Anglia 1 0.82213   0.16617   0.95053   0.46386   22   B   usable mapping rate illumina novaseq_era 3prime poly_a lexogen bulk unknown unknown   United Kingdom 2023-08-30 Adult Adult Blood Hematopoietic System
25313 25313 SRR25793385 SRX21515629 SRS18742880 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.       RNA seq Erythrocytes miR 144 adult miR 144 adult   isolate:miR 144 mutant|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal                 Quant seq Erythrocytes miR 144 mutant Danio rerio ADULT replicate 2 144 2 adult blood 144 2 adult blood Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457465     DC-144AL2_S11.fastq fastq 497890134.0 10636306.0 DC 144AL2 S11.fastq 0:46.81 A:134598214;C:94036725;G:109501897;T:158719603;N:1033695 46       134598214 94036725 109501897 158719603 1033695 SRX21515629 SRS18742880 SRA1701831 University of East Anglia|Biological Sciences University of East Anglia 1 0.88496   0.29132   0.96002   0.53343   22   B   usable mapping rate illumina novaseq_era 3prime poly_a lexogen bulk unknown unknown   United Kingdom 2023-08-30 Adult Adult Blood Hematopoietic System
25314 25314 SRR25793386 SRX21515628 SRS18742879 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.       RNA seq Erythrocytes Wild type embryo WT embryo   isolate:Wildtype|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal                 Quant seq Erythrocytes Wild type Danio rerio 2 dpf replicate 2 WT2 embryo blood WT2 embryo blood Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457465     DC-WTE2_S14.fastq fastq 250958009.0 9755304.0 DC WTE2 S14.fastq 0:25.73 A:43225839;C:41823862;G:54150092;T:43159724;N:68598492 25       43225839 41823862 54150092 43159724 68598492 SRX21515628 SRS18742879 SRA1701831 University of East Anglia|Biological Sciences University of East Anglia 1 0.34114   0.05466   0.96664   0.54625   47   B   usable mapping rate illumina novaseq_era 3prime poly_a lexogen bulk unknown unknown   United Kingdom 2023-08-30 Hatching Embryo Blood Hematopoietic System
25315 25315 SRR25793387 SRX21515627 SRS18742879 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.       RNA seq Erythrocytes Wild type embryo WT embryo   isolate:Wildtype|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal                 Quant seq Erythrocytes Wild type Danio rerio 2 dpf replicate 1 WT1 embryo blood WT1 embryo blood Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP457465     DC-WTE1_S13.fastq fastq 816518564.0 19556325.0 DC WTE1 S13.fastq 0:41.75 A:187091550;C:151287428;G:179967901;T:221475884;N:76695801 41       187091550 151287428 179967901 221475884 76695801 SRX21515627 SRS18742879 SRA1701831 University of East Anglia|Biological Sciences University of East Anglia 1 0.61681   0.1874   0.95101   0.56879   29   B   usable mapping rate illumina novaseq_era 3prime poly_a lexogen bulk unknown unknown   United Kingdom 2023-08-30 Hatching 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
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
38257 38257 SRR1609758 SRX730411 SRS719632 SRP048807 PRJNA263496 Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish GSE62221 Transcriptome Analysis The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures ranging from normal 28°C to mild 18°C and severe 10°C cold using RNA seq. The tissues varied in the number of cold responsive genes of which the kidney appeared to be most sensitive whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes such as RNA splicing and proton transport as well tissue specific processes such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program DREME. Eleven motifs 6 known and 5 novel were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs such as the AP 1 and STAT1 binding sites are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures   pubmed:26227973   spleen10 GSM1523053   source name:spleen|tissue:spleen|temperature:10°C|strain:Tubingen|age:6 mpf spleen10 Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html which is a python based script was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... spleen fish were maintained 12h to adapt low temperatures and then killed by pithing Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:spleen|temperature:10°C|strain:Tubingen|age:6 mpf GSM1523053 GSM1523053: spleen10; Danio rerio; RNA Seq GSM1523053   1 Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1523053 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP048807     spleen10_2.fq.gz spleen10_1.fq.gz fastq fastq 5089614600.0 25448073.0 GSM1523053 r1 0:100 1:100 A:1315179584;C:1230198758;G:1227165313;T:1316987828;N:83117 100 100     1315179584 1230198758 1227165313 1316987828 83117 SRX730411 SRS719632 SRA189240 GEO Shanghai Ocean University 2 0.9612 0.9561 0.04114 0.04116 0.77518 0.77926 0.42558 0.42199 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   China 2014-10-09 Adult Adult Spleen Hematopoietic System
38258 38258 SRR1609757 SRX730410 SRS719631 SRP048807 PRJNA263496 Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish GSE62221 Transcriptome Analysis The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures ranging from normal 28°C to mild 18°C and severe 10°C cold using RNA seq. The tissues varied in the number of cold responsive genes of which the kidney appeared to be most sensitive whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes such as RNA splicing and proton transport as well tissue specific processes such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program DREME. Eleven motifs 6 known and 5 novel were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs such as the AP 1 and STAT1 binding sites are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures   pubmed:26227973   spleen18 GSM1523052   source name:spleen|tissue:spleen|temperature:18°C|strain:Tubingen|age:6 mpf spleen18 Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html which is a python based script was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... spleen fish were maintained 12h to adapt low temperatures and then killed by pithing Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:spleen|temperature:18°C|strain:Tubingen|age:6 mpf GSM1523052 GSM1523052: spleen18; Danio rerio; RNA Seq GSM1523052   1 Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1523052 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP048807     spleen18_1.fq.gz spleen18_2.fq.gz fastq fastq 4494055400.0 22470277.0 GSM1523052 r1 0:100 1:100 A:1167396911;C:1079923943;G:1078183614;T:1168479101;N:71831 100 100     1167396911 1079923943 1078183614 1168479101 71831 SRX730410 SRS719631 SRA189240 GEO Shanghai Ocean University 2 0.96809 0.96224 0.02675 0.02626 0.80012 0.80369 0.28419 0.28966 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   China 2014-10-09 Adult Adult Spleen Hematopoietic System
38259 38259 SRR1609756 SRX730409 SRS719630 SRP048807 PRJNA263496 Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish GSE62221 Transcriptome Analysis The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures ranging from normal 28°C to mild 18°C and severe 10°C cold using RNA seq. The tissues varied in the number of cold responsive genes of which the kidney appeared to be most sensitive whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes such as RNA splicing and proton transport as well tissue specific processes such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program DREME. Eleven motifs 6 known and 5 novel were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs such as the AP 1 and STAT1 binding sites are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures   pubmed:26227973   spleen28 GSM1523051   source name:spleen|tissue:spleen|temperature:28°C|strain:Tubingen|age:6 mpf spleen28 Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html which is a python based script was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... spleen fish were maintained 12h to adapt low temperatures and then killed by pithing Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:spleen|temperature:28°C|strain:Tubingen|age:6 mpf GSM1523051 GSM1523051: spleen28; Danio rerio; RNA Seq GSM1523051   1 Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1523051 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP048807     spleen28_2.fq.gz spleen28_1.fq.gz fastq fastq 3499734800.0 17498674.0 GSM1523051 r1 0:100 1:100 A:912324481;C:841616616;G:837795621;T:907938558;N:59524 100 100     912324481 841616616 837795621 907938558 59524 SRX730409 SRS719630 SRA189240 GEO Shanghai Ocean University 2 0.95732 0.95047 0.04767 0.04837 0.75507 0.7613 0.5152 0.51185 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   China 2014-10-09 Adult Adult Spleen Hematopoietic System
38293 38293 SRR1647684 SRX756919 SRS742121 SRP049663 PRJNA266803 Spring Varaemia of Carp Virus SVCV infection of adult zebrafish GSE63133 Transcriptome Analysis During viral infection a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection i.e. 6h and 24h post infection. For 12 zebrafish IRFs we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7 which together with DrIRF3 was highly induced by SVCV infection. For type I IFNs zebrafish has four IFN genes three of which IFN1/2/3 particularly IFN 1 and IFN 3 were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately 50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.   pubmed:25535281   24S GSM1541908   source name:spleen|tissue:spleen|disease state:24h post SVCV infection 24S Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... spleen   Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:spleen|disease state:24h post SVCV infection GSM1541908 GSM1541908: 24S; Danio rerio; RNA Seq GSM1541908   1 Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1541908 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP049663     24S_ATGTCA_L003_R1.fastq fastq 1207014756.0 23666956.0 GSM1541908 r1 0:51 A:316359100;C:290453604;G:283305513;T:316815698;N:80841 51       316359100 290453604 283305513 316815698 80841 SRX756919 SRS742121 SRA200717 GEO Institute of Hydrobiology, Chinese Academy of Sciences 1 0.91158   0.09021   0.70867   0.46907   51   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-11-10 Undetermined Adult Spleen Hematopoietic System
38294 38294 SRR1647683 SRX756918 SRS742119 SRP049663 PRJNA266803 Spring Varaemia of Carp Virus SVCV infection of adult zebrafish GSE63133 Transcriptome Analysis During viral infection a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection i.e. 6h and 24h post infection. For 12 zebrafish IRFs we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7 which together with DrIRF3 was highly induced by SVCV infection. For type I IFNs zebrafish has four IFN genes three of which IFN1/2/3 particularly IFN 1 and IFN 3 were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately 50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.   pubmed:25535281   6S GSM1541907   source name:spleen|tissue:spleen|disease state:6h post SVCV infection 6S Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... spleen   Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:spleen|disease state:6h post SVCV infection GSM1541907 GSM1541907: 6S; Danio rerio; RNA Seq GSM1541907   1 Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1541907 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP049663     6S_AGTTCC_L003_R1.fastq fastq 1251006540.0 24529540.0 GSM1541907 r1 0:51 A:323805792;C:303846999;G:297418642;T:325862442;N:72665 51       323805792 303846999 297418642 325862442 72665 SRX756918 SRS742119 SRA200717 GEO Institute of Hydrobiology, Chinese Academy of Sciences 1 0.92105   0.09005   0.71273   0.46937   51   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-11-10 Undetermined Adult Spleen Hematopoietic System
38295 38295 SRR1647682 SRX756917 SRS742118 SRP049663 PRJNA266803 Spring Varaemia of Carp Virus SVCV infection of adult zebrafish GSE63133 Transcriptome Analysis During viral infection a large number of immune response signaling molecules including the interferon regulatory IRF family and type I interferon IFN transcribe. The exact identity and expression levels of fish IRFs and type I IFNs during viral infection remains largely unknown. Here we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type I IFNs during two stages of SVCV infection i.e. 6h and 24h post infection. For 12 zebrafish IRFs we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV infected tissues but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7 which together with DrIRF3 was highly induced by SVCV infection. For type I IFNs zebrafish has four IFN genes three of which IFN1/2/3 particularly IFN 1 and IFN 3 were significantly transcribed under the same conditions. Overall design: 12 adult healthy male and female 1:1 zebrafish were infected by intraperitoneal inoculation with approximately 50 µL SVCV 10 8TCID50/mL. 6 infected fish male:female=1:1 were sacrificed at 6h post injection and 6 male:female=1:1 were sacrificed at 24h post injection for head kidney 6K and 24K and spleen 6S and 24S. Head kidney and spleen 0K and 0S from the 6 control adult zebrafish male:female=1:1 were collected as negative control.   pubmed:25535281   0S GSM1541906   source name:spleen|tissue:spleen|disease state:un infected 0S Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: mm8 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... spleen   Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:spleen|disease state:un infected GSM1541906 GSM1541906: 0S; Danio rerio; RNA Seq GSM1541906   1 Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1541906 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP049663     0S_AGTCAA_L003_R1.fastq fastq 1155087372.0 22648772.0 GSM1541906 r1 0:51 A:301183546;C:279328135;G:272663981;T:301834798;N:76912 51       301183546 279328135 272663981 301834798 76912 SRX756917 SRS742118 SRA200717 GEO Institute of Hydrobiology, Chinese Academy of Sciences 1 0.91841   0.09679   0.70546   0.47624   51   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2014-11-10 Undetermined Adult Spleen Hematopoietic System
39665 39665 SRR2027911 SRX1029315 SRS937775 SRP058376 PRJNA284108 RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures GSE68920 Transcriptome Analysis We used different zebrafish transgenic lines to sort macrophages neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis amplification and library preparation were performed as previously described. Rougeot et al. 2014 Methods Mol Biol 1197:41 66.   pubmed:31832066   6dpf mpeg1:mCherryPosMmarinumGFPPos rep3 GSM1686459   source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu 6dpf mpeg1:mCherryPosMmarinumGFPPos rep3 Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample zebra fish larvae Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides. Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu GSM1686459 GSM1686459: 6dpf mpeg1:mCherryPosMmarinumGFPPos rep3; Danio rerio; RNA Seq GSM1686459   1 Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides. GEO Accession:GSM1686459 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP058376     ZFG-14-09_06_ATTCCT_L003_R1_001.fastq.gz fastq 988427889.0 19380939.0 GSM1686459 r1 0:51 A:322268594;C:166925867;G:171531103;T:327506982;N:195343 51       322268594 166925867 171531103 327506982 195343 SRX1029315 SRS937775 SRA268539 GEO Institute of Biology, Leiden University 1 0.6999   0.24019   0.85358   0.56832   51   B   usable mapping rate illumina hiseq_era full_length poly_a smarter bulk unknown unknown   Netherlands 2015-05-15 Larval Larval Blood Hematopoietic System
39666 39666 SRR2027910 SRX1029314 SRS937773 SRP058376 PRJNA284108 RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures GSE68920 Transcriptome Analysis We used different zebrafish transgenic lines to sort macrophages neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis amplification and library preparation were performed as previously described. Rougeot et al. 2014 Methods Mol Biol 1197:41 66.   pubmed:31832066   6dpf mpeg1:mCherryPosMmarinumGFPPos rep2 GSM1686458   source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu 6dpf mpeg1:mCherryPosMmarinumGFPPos rep2 Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample zebra fish larvae Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides. Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu GSM1686458 GSM1686458: 6dpf mpeg1:mCherryPosMmarinumGFPPos rep2; Danio rerio; RNA Seq GSM1686458   1 Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides. GEO Accession:GSM1686458 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP058376     ZFG-14-09_05_ACTGAT_L003_R1_001.fastq.gz fastq 846771207.0 16603357.0 GSM1686458 r1 0:51 A:268435928;C:150903620;G:153931870;T:273331733;N:168056 51       268435928 150903620 153931870 273331733 168056 SRX1029314 SRS937773 SRA268539 GEO Institute of Biology, Leiden University 1 0.72025   0.17943   0.87937   0.5683   51   B   usable mapping rate illumina hiseq_era full_length poly_a smarter bulk unknown unknown   Netherlands 2015-05-15 Larval Larval Blood Hematopoietic System
39667 39667 SRR2027909 SRX1029313 SRS937774 SRP058376 PRJNA284108 RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures GSE68920 Transcriptome Analysis We used different zebrafish transgenic lines to sort macrophages neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis amplification and library preparation were performed as previously described. Rougeot et al. 2014 Methods Mol Biol 1197:41 66.   pubmed:31832066   6dpf mpeg1:mCherryPosMmarinumGFPPos rep1 GSM1686457   source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu 6dpf mpeg1:mCherryPosMmarinumGFPPos rep1 Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample zebra fish larvae Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides. Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu GSM1686457 GSM1686457: 6dpf mpeg1:mCherryPosMmarinumGFPPos rep1; Danio rerio; RNA Seq GSM1686457   1 Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides. GEO Accession:GSM1686457 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP058376     ZFG-14-09_04_GAGTGG_L003_R1_001.fastq.gz fastq 807459642.0 15832542.0 GSM1686457 r1 0:51 A:260516660;C:140425216;G:145411663;T:260942267;N:163836 51       260516660 140425216 145411663 260942267 163836 SRX1029313 SRS937774 SRA268539 GEO Institute of Biology, Leiden University 1 0.7097   0.17187   0.93304   0.64092   51   B   usable mapping rate illumina hiseq_era full_length poly_a smarter bulk unknown unknown   Netherlands 2015-05-15 Larval Larval Blood Hematopoietic System
39668 39668 SRR2027908 SRX1029312 SRS937776 SRP058376 PRJNA284108 RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures GSE68920 Transcriptome Analysis We used different zebrafish transgenic lines to sort macrophages neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis amplification and library preparation were performed as previously described. Rougeot et al. 2014 Methods Mol Biol 1197:41 66.   pubmed:31832066   6dpf mpeg1:mCherryPos MmarinumGFPNeg rep3 GSM1686456   source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu 6dpf mpeg1:mCherryPos MmarinumGFPNeg rep3 Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample zebra fish larvae Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides. Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu GSM1686456 GSM1686456: 6dpf mpeg1:mCherryPos MmarinumGFPNeg rep3; Danio rerio; RNA Seq GSM1686456   1 Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides. GEO Accession:GSM1686456 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP058376     ZFG-14-09_03_CGTACG_L003_R1_001.fastq.gz fastq 1523483526.0 29872226.0 GSM1686456 r1 0:51 A:499019794;C:267493952;G:277264815;T:479405699;N:299266 51       499019794 267493952 277264815 479405699 299266 SRX1029312 SRS937776 SRA268539 GEO Institute of Biology, Leiden University 1 0.67328   0.15117   0.91179   0.54858   51   B   usable mapping rate illumina hiseq_era full_length poly_a smarter bulk unknown unknown   Netherlands 2015-05-15 Larval Larval Blood Hematopoietic System
39669 39669 SRR2027907 SRX1029311 SRS937777 SRP058376 PRJNA284108 RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures GSE68920 Transcriptome Analysis We used different zebrafish transgenic lines to sort macrophages neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis amplification and library preparation were performed as previously described. Rougeot et al. 2014 Methods Mol Biol 1197:41 66.   pubmed:31832066   6dpf mpeg1:mCherryPos MmarinumGFPNeg rep2 GSM1686455   source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu 6dpf mpeg1:mCherryPos MmarinumGFPNeg rep2 Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample zebra fish larvae Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides. Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu GSM1686455 GSM1686455: 6dpf mpeg1:mCherryPos MmarinumGFPNeg rep2; Danio rerio; RNA Seq GSM1686455   1 Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides. GEO Accession:GSM1686455 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP058376     ZFG-14-09_02_GTTTCG_L003_R1_001.fastq.gz fastq 938675094.0 18405394.0 GSM1686455 r1 0:51 A:284384359;C:173449465;G:178039777;T:302612825;N:188668 51       284384359 173449465 178039777 302612825 188668 SRX1029311 SRS937777 SRA268539 GEO Institute of Biology, Leiden University 1 0.72884   0.14723   0.90767   0.57414   51   B   usable mapping rate illumina hiseq_era full_length poly_a smarter bulk unknown unknown   Netherlands 2015-05-15 Larval Larval Blood Hematopoietic System
39670 39670 SRR2027906 SRX1029310 SRS937778 SRP058376 PRJNA284108 RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures GSE68920 Transcriptome Analysis We used different zebrafish transgenic lines to sort macrophages neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis amplification and library preparation were performed as previously described. Rougeot et al. 2014 Methods Mol Biol 1197:41 66.   pubmed:31832066   6dpf mpeg1:mCherryPos MmarinumGFPNeg rep1 GSM1686454   source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu 6dpf mpeg1:mCherryPos MmarinumGFPNeg rep1 Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample zebra fish larvae Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides. Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu GSM1686454 GSM1686454: 6dpf mpeg1:mCherryPos MmarinumGFPNeg rep1; Danio rerio; RNA Seq GSM1686454   1 Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc. San Diego USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides. GEO Accession:GSM1686454 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP058376     ZFG-14-09_01_GTGGCC_L003_R1_001.fastq.gz fastq 1248324348.0 24476948.0 GSM1686454 r1 0:51 A:391067882;C:223380294;G:229132022;T:404526410;N:217740 51       391067882 223380294 229132022 404526410 217740 SRX1029310 SRS937778 SRA268539 GEO Institute of Biology, Leiden University 1 0.70232   0.14257   0.92894   0.59305   51   B   usable mapping rate illumina hiseq_era full_length poly_a smarter bulk unknown unknown   Netherlands 2015-05-15 Larval Larval Blood Hematopoietic System
39974 39974 SRR2726604 SRX1354695 SRS1121101 SRP064895 PRJNA298967 Danio rerio Raw sequence reads PRJNA298967 Whole Genome Sequencing Alternative polyadenylation in the anti bacterial immune response of zebrafish         UC.fq.gz   breed:missing|cultivar:missing|ecotype:missing|isolate:missing|strain:missing|age:6 month|dev stage:adult|sex:male|tissue:spleen|BioSampleModel:Model organism or animal                 Alternative polyadenylation in the anti bacterial immune response of zebrafish UC 298967 SAPAS three prime cDNA library     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>55</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP064895     UC.fq.gz fastq 908330752.0 16220192.0 UC 0:56 A:268296300;C:164753303;G:152582935;T:321764605;N:933609 56       268296300 164753303 152582935 321764605 933609 SRX1354695 SRS1121101 SRA305678 Sun Yat-Sen University|Department of Biochemistry, College of Life Scienc Sun Yat-Sen University 1 0.76113   0.14836   0.86764   0.49191   56   B   usable mapping rate illumina early_illumina unknown random_priming unknown bulk unknown unknown   China 2015-10-19 Adult Adult Spleen Hematopoietic System
39975 39975 SRR2726605 SRX1343023 SRS1117908 SRP064895 PRJNA298967 Danio rerio Raw sequence reads PRJNA298967 Whole Genome Sequencing Alternative polyadenylation in the anti bacterial immune response of zebrafish         BC.fq.gz   breed:missing|cultivar:missing|ecotype:missing|isolate:missing|strain:missing|age:6 month|dev stage:adult|sex:male|tissue:spleen|health state:health|sample type:tissue sample|BioSampleModel:Model organism or animal                 Alternative polyadenylation in the anti bacterial immune response of zebrafish 298967 298967 SAPAS three prime cDNA library     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>55</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP064895     BC.fq.gz fastq 613456536.0 10954581.0 BC 0:56 A:184952368;C:111595938;G:99647506;T:216155456;N:1105268 56       184952368 111595938 99647506 216155456 1105268 SRX1343023 SRS1117908 SRA305678 Sun Yat-Sen University|Department of Biochemistry, College of Life Scienc Sun Yat-Sen University 1 0.74636   0.11848   0.84678   0.47133   56   B   usable mapping rate illumina early_illumina unknown random_priming unknown bulk unknown unknown   China 2015-10-24 Adult Adult Spleen 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
40830 40830 SRR3381828 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_s5_1_GSLv3-7_33_SL139790.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_33_SL139790.fastq.gz fastq fastq 701940200.0 7019402.0 GSM2122866 r4 0:50 1:50 A:194036996;C:155992188;G:155284640;T:196613376;N:13000 50 50     194036996 155992188 155284640 196613376 13000 SRX1704275 SRS1396348 SRA411416 GEO Molecular and Biomedical Sciences, University of Maine 2 0.90959 0.91386 0.16429 0.17705 0.75544 0.7391 0.548 0.57224 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
40831 40831 SRR3381829 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     C8DKGANXX_s8_1_GSLv3-7_33_SL139790.fastq.gz C8DKGANXX_s8_2_GSLv3-7_33_SL139790.fastq.gz fastq fastq 1596331500.0 15963315.0 GSM2122866 r5 0:50 1:50 A:444854958;C:353331559;G:354367449;T:442888766;N:888768 50 50     444854958 353331559 354367449 442888766 888768 SRX1704275 SRS1396348 SRA411416 GEO Molecular and Biomedical Sciences, University of Maine 2 0.90554 0.91175 0.17327 0.17968 0.73669 0.73728 0.55044 0.5651 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
40832 40832 SRR3381830 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     C8DKGANXX_s7_1_GSLv3-7_33_SL139790.fastq.gz C8DKGANXX_s7_2_GSLv3-7_33_SL139790.fastq.gz fastq fastq 1600754600.0 16007546.0 GSM2122866 r6 0:50 1:50 A:446178544;C:354456079;G:355435947;T:443937350;N:746680 50 50     446178544 354456079 355435947 443937350 746680 SRX1704275 SRS1396348 SRA411416 GEO Molecular and Biomedical Sciences, University of Maine 2 0.90709 0.91238 0.17011 0.17723 0.74054 0.73994 0.55938 0.55607 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
41032 41032 SRR3581739 SRX1797279 SRS1465200 SRP075626 PRJNA322629 Mycobacterial infection of adult zebrafish PRJNA322629 Other RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.       Larval non fluorescent cells post macrophage sorting3 C NF3   breed:*AB|age:4dpf|dev stage:Larval|sex:not determined|tissue:Whole animal following macrophage depletion via FACS|BioSampleModel:Model organism or animal                 C NF3 C NF3 C NF3 1     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP075626     C_NF3.fastq.gz fastq 1745512893.0 34225743.0 C NF3.fastq.gz 0:51 A:470456301;C:396221813;G:401458508;T:477287506;N:88765 51       470456301 396221813 401458508 477287506 88765 SRX1797279 SRS1465200 SRA429046 Duke University|Molecular Genetics &amp; Microbiology Duke University 1 0.92839   0.06821   0.73099   0.44395   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2016-05-25 Larval Larval Blood Hematopoietic System
41033 41033 SRR3581729 SRX1797278 SRS1465199 SRP075626 PRJNA322629 Mycobacterial infection of adult zebrafish PRJNA322629 Other RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.       Larval non fluorescent cells post macrophage sorting2 C NF2   breed:*AB|age:4dpf|dev stage:Larval|sex:not determined|tissue:Whole animal following macrophage depletion via FACS|BioSampleModel:Model organism or animal                 C NF2 C NF2 C NF2 1     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP075626     C_NF2.fastq.gz fastq 2116510506.0 41500206.0 C NF2.fastq.gz 0:51 A:580244434;C:475940957;G:474848964;T:585459729;N:16422 51       580244434 475940957 474848964 585459729 16422 SRX1797278 SRS1465199 SRA429045 Duke University|Molecular Genetics &amp; Microbiology Duke University 1 0.90388   0.06926   0.78963   0.49501   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2017-06-24 Larval Larval Blood Hematopoietic System
41034 41034 SRR3581718 SRX1797274 SRS1465196 SRP075626 PRJNA322629 Mycobacterial infection of adult zebrafish PRJNA322629 Other RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.       Larval non fluorescent cells post macrophage sorting1 C NF1   breed:*AB|age:4dpf|dev stage:Larval|sex:not determined|tissue:Whole animal following macrophage depletion via FACS|BioSampleModel:Model organism or animal                 C NF1 C NF1 C NF1 1     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP075626     C_NF1.fastq.gz fastq 1492422690.0 29263190.0 C NF1.fastq.gz 0:51 A:421145406;C:327412398;G:328273236;T:415327504;N:264146 51       421145406 327412398 328273236 415327504 264146 SRX1797274 SRS1465196 SRA429041 Duke University|Molecular Genetics &amp; Microbiology Duke University 1 0.82347   0.08561   0.75207   0.45637   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2017-06-24 Larval Larval Blood Hematopoietic System
41038 41038 SRR3581671 SRX1797269 SRS1465191 SRP075626 PRJNA322629 Mycobacterial infection of adult zebrafish PRJNA322629 Other RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.       Fluorescence activated cell sorted macrophages1 iRed1   breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Fluorescence activated cell sorted macrophages|BioSampleModel:Model organism or animal                 iRed1 iRed1 iRed1 1     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP075626     iRed1.fastq.gz fastq 2227229772.0 43671172.0 iRed1.fastq.gz 0:51 A:643185725;C:477251583;G:480258902;T:626515881;N:17681 51       643185725 477251583 480258902 626515881 17681 SRX1797269 SRS1465191 SRA429036 Duke University|Molecular Genetics &amp; Microbiology Duke University 1 0.88005   0.11318   0.76197   0.49474   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2017-06-24 Adult Adult Blood Hematopoietic System
41039 41039 SRR3581670 SRX1797268 SRS1465190 SRP075626 PRJNA322629 Mycobacterial infection of adult zebrafish PRJNA322629 Other RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.       D rerio dissected M marinum granuloma5 disGran5   breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Dissected granuloma|BioSampleModel:Model organism or animal                 disGran5 disGran5 disGran5 1     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP075626     disGran5.fastq.gz fastq 2097698850.0 41131350.0 disGran5.fastq.gz 0:51 A:606466942;C:449212134;G:448063993;T:593938942;N:16839 51       606466942 449212134 448063993 593938942 16839 SRX1797268 SRS1465190 SRA429035 Duke University|Molecular Genetics &amp; Microbiology Duke University 1 0.89212   0.09154   0.76788   0.51096   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2017-06-24 Adult Adult Blood Hematopoietic System
41040 41040 SRR3581669 SRX1797267 SRS1465187 SRP075626 PRJNA322629 Mycobacterial infection of adult zebrafish PRJNA322629 Other RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.       D rerio dissected M marinum granuloma4 disGran4   breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Dissected granuloma|BioSampleModel:Model organism or animal                 disGran4 disGran4 disGran4 1     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP075626     disGran4.fastq.gz fastq 2969920485.0 58233735.0 disGran4.fastq.gz 0:51 A:861895830;C:635643178;G:635675729;T:836681349;N:24399 51       861895830 635643178 635675729 836681349 24399 SRX1797267 SRS1465187 SRA429034 Duke University|Molecular Genetics &amp; Microbiology Duke University 1 0.87215   0.09876   0.7498   0.55116   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2017-06-24 Adult Adult Blood Hematopoietic System
41041 41041 SRR3581668 SRX1797266 SRS1465186 SRP075626 PRJNA322629 Mycobacterial infection of adult zebrafish PRJNA322629 Other RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.       D rerio dissected M marinum granuloma3 disGran3   breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Dissected granuloma|BioSampleModel:Model organism or animal                 disGran3 disGran3 disGran3 1     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP075626     disGran3.fastq.gz fastq 2398905207.0 47037357.0 disGran3.fastq.gz 0:51 A:693817641;C:513302774;G:516121702;T:675643798;N:19292 51       693817641 513302774 516121702 675643798 19292 SRX1797266 SRS1465186 SRA429033 Duke University|Molecular Genetics &amp; Microbiology Duke University 1 0.88631   0.10719   0.75465   0.51255   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2017-06-24 Adult Adult Blood Hematopoietic System
41042 41042 SRR3581667 SRX1797265 SRS1465185 SRP075626 PRJNA322629 Mycobacterial infection of adult zebrafish PRJNA322629 Other RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.       D rerio dissected M marinum granuloma2 disGran2   breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Dissected granuloma|BioSampleModel:Model organism or animal                 disGran2 disGran2 disGran2 1     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP075626     disGran2.fastq.gz fastq 2108649213.0 41346063.0 disGran2.fastq.gz 0:51 A:606624392;C:457029369;G:459017347;T:585961261;N:16844 51       606624392 457029369 459017347 585961261 16844 SRX1797265 SRS1465185 SRA429032 Duke University|Molecular Genetics &amp; Microbiology Duke University 1 0.88259   0.10405   0.74282   0.536   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2017-06-24 Adult Adult Blood Hematopoietic System
41043 41043 SRR3581315 SRX1797076 SRS1465045 SRP075626 PRJNA322629 Mycobacterial infection of adult zebrafish PRJNA322629 Other RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.       D rerio dissected M marinum granuloma1 disGran1   breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Dissected granuloma|BioSampleModel:Model organism or animal                 disGran1 disGran1 disGran1 1     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP075626     disGran1.fastq.gz fastq 2529627234.0 49600534.0 disGran1.fastq.gz 0:51 A:738849065;C:530442613;G:521673896;T:738641232;N:20428 51       738849065 530442613 521673896 738641232 20428 SRX1797076 SRS1465045 SRA428910 Duke University|Molecular Genetics &amp; Microbiology Duke University 1 0.81713   0.09754   0.75213   0.51283   51   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   United States 2017-07-24 Adult Adult Blood Hematopoietic System
44935 44935 SRR6308293 SRX3408679 SRS2701475 SRP125291 PRJNA419036 Danio rerio strain:ASWT Transcriptome or Gene expression PRJNA419036 Other A genome wide map of circular RNA in adult zebrafish.       Zf blood Zf blood   strain:ASWT|age:1year|sex:male|tissue:Blood|BioSampleModel:Model organism or animal                 A genome wide map of circular RNA in adult zebrafish Zf blood Zf blood Tissue were isolated from adult zebrafish anaesthetized using 0.004% Tricaine Sigma USA. Extreme care was taken to avoid contamination to obtain pure homogenous tissue samples. The tissues were repeatedly washed in PBS to remove contaminating debris. The tissue samples were homogenized in Trizol for cell lysis Invitrogen USA. RNA was isolated from the homogenized tissue samples using RNeasy kit Qiagen USA. Sample preparation for sequencing was carried out using Truseq stranded RNA sample preparation kit Illumina USA as per supplier's instructions. In order to remove the ribosomal RNA rRNA one microgram of total RNA was hybridised with Ribo zero gold rRNA removal probe. Upon removing rRNA the samples were processed for fragmentation in the presence of ionic cations at 37 degree Celcius. First stranded complementary DNA cDNA was prepared by random hexamers and superscript II reverse transcriptase Invitrogen USA in presence of Actinomycin D to facilitate RNA dependent synthesis for improving strand specificity. The second strand was synthesised with second strand cDNA mix containing dUTP instead of dTTP and subjected to A base addition followed by adapter ligation. Final libraries were prepared by amplifying adapter ligated double strand cDNA. Clusters were generated on Hiseq flow cell v3 Illumina in cBot according to standard protocol Illumina USA.     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP125291     Zf_blood_R1.fastq Zf_blood_R2.fastq fastq fastq 3815054252.0 20461146.0 Zf blood R1.fastq 0:97.58 1:88.87 A:1003195592;C:903122443;G:887002461;T:1021496839;N:236917 97 88     1003195592 903122443 887002461 1021496839 236917 SRX3408679 SRS2701475 SRA631861 CSIR-Institute of Genomics and Integrative Biology|Genomic Medicine CSIR-Institute of Genomics and Integrative Biology 2 0.88344 0.89187 0.31874 0.32265 0.75398 0.75706 0.6181 0.61725 100 54 B B biological fallback assumption illumina hiseq_era unknown random_priming ribozero bulk unknown unknown   India 2017-11-20 Adult Adult Blood Hematopoietic System
47583 47583 SRR6661157 SRX3638253 SRS2904504 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   SplWTPHZ 3 GSM2975201   source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type SplWTPHZ 3 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type GSM2975201 GSM2975201: SplWTPHZ 3; Danio rerio; RNA Seq GSM2975201   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975201 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     SplWTPHZ_3.fastq.gz fastq 863137362.0 16924262.0 GSM2975201 r1 0:51 A:243029420;C:186621398;G:190769119;T:242704294;N:13131 51       243029420 186621398 190769119 242704294 13131 SRX3638253 SRS2904504 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.94871   0.18797   0.7289   0.48689   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Spleen Hematopoietic System
47584 47584 SRR6661156 SRX3638252 SRS2904503 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   SplWTPHZ 2 GSM2975200   source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type SplWTPHZ 2 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type GSM2975200 GSM2975200: SplWTPHZ 2; Danio rerio; RNA Seq GSM2975200   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975200 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     SplWTPHZ_2.fastq.gz fastq 748057494.0 14667794.0 GSM2975200 r1 0:51 A:212731080;C:159238564;G:163993235;T:212082953;N:11662 51       212731080 159238564 163993235 212082953 11662 SRX3638252 SRS2904503 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.94641   0.22364   0.7264   0.48998   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Spleen Hematopoietic System
47585 47585 SRR6661155 SRX3638251 SRS2904502 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   SplWTPHZ 1 GSM2975199   source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type SplWTPHZ 1 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type GSM2975199 GSM2975199: SplWTPHZ 1; Danio rerio; RNA Seq GSM2975199   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975199 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     SplWTPHZ_1.fastq.gz fastq 771862917.0 15134567.0 GSM2975199 r1 0:51 A:220317243;C:164032479;G:167543123;T:219958265;N:11807 51       220317243 164032479 167543123 219958265 11807 SRX3638251 SRS2904502 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.94835   0.1926   0.71453   0.48677   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Spleen Hematopoietic System
47586 47586 SRR6661154 SRX3638250 SRS2904501 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   SplWT 3 GSM2975198   source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type SplWT 3 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type GSM2975198 GSM2975198: SplWT 3; Danio rerio; RNA Seq GSM2975198   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975198 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     SplWT_3.fastq.gz fastq 815973888.0 15999488.0 GSM2975198 r1 0:51 A:236186435;C:169473350;G:175246943;T:235055142;N:12018 51       236186435 169473350 175246943 235055142 12018 SRX3638250 SRS2904501 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.94554   0.25855   0.71873   0.54675   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Spleen Hematopoietic System
47587 47587 SRR6661153 SRX3638249 SRS2904499 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   SplWT 2 GSM2975197   source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type SplWT 2 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type GSM2975197 GSM2975197: SplWT 2; Danio rerio; RNA Seq GSM2975197   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975197 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     SplWT_2.fastq.gz fastq 909644262.0 17836162.0 GSM2975197 r1 0:51 A:259661486;C:192636111;G:198048163;T:259284494;N:14008 51       259661486 192636111 198048163 259284494 14008 SRX3638249 SRS2904499 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.94781   0.22979   0.69962   0.49839   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Spleen Hematopoietic System
47588 47588 SRR6661152 SRX3638248 SRS2904500 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   SplWT 1 GSM2975196   source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type SplWT 1 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:spleen|age:5 mpf 6 mpf|genotype:Wild type GSM2975196 GSM2975196: SplWT 1; Danio rerio; RNA Seq GSM2975196   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975196 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     SplWT_1.fastq.gz fastq 888755274.0 17426574.0 GSM2975196 r1 0:51 A:241072815;C:200347978;G:205733626;T:241587449;N:13406 51       241072815 200347978 205733626 241587449 13406 SRX3638248 SRS2904500 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.95759   0.1342   0.72918   0.52233   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Spleen Hematopoietic System
47589 47589 SRR6661151 SRX3638247 SRS2904498 SRP131956 PRJNA432507 Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne GSE109978 Transcriptome Analysis RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys.   pubmed:30248094   SplDKOPHZ 3 GSM2975195   source name:whole animal|tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO SplDKOPHZ 3 Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. whole animal Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation Normal zebrafish husbandary tissue:spleen|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO GSM2975195 GSM2975195: SplDKOPHZ 3; Danio rerio; RNA Seq GSM2975195   1 TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation GEO Accession:GSM2975195 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP131956     SplDKOPHZ_3.fastq.gz fastq 881441160.0 17283160.0 GSM2975195 r1 0:51 A:243254581;C:194198200;G:199055092;T:244919975;N:13312 51       243254581 194198200 199055092 244919975 13312 SRX3638247 SRS2904498 SRA654641 GEO Laboratory of Molecular Biology, NIH/NIDDK 1 0.90441   0.14881   0.71447   0.51129   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   United States 2018-02-01 Adult Adult Spleen Hematopoietic System

Next page

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

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