{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Embryo\" and tissue_curation_coarse = \"Hematopoietic System\"", "rows": [[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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing", "ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 12", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "NextSeq 500", null, "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, null, null, 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", null, "United Kingdom", "2018-03-14", "Undetermined", "Embryo", "Blood", "Hematopoietic System"], [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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing", "ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 11", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "NextSeq 500", null, "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, null, null, 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", null, "United Kingdom", "2018-03-14", "Undetermined", "Embryo", "Blood", "Hematopoietic System"], [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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing", "ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 10", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "NextSeq 500", null, "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, null, null, 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", null, "United Kingdom", "2018-03-14", "Undetermined", "Embryo", "Blood", "Hematopoietic System"], [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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing", "ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 9", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "NextSeq 500", null, "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, null, null, 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", null, "United Kingdom", "2018-03-14", "Undetermined", "Embryo", "Blood", "Hematopoietic System"], [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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing", "ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 8", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "NextSeq 500", null, "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, null, null, 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", null, "United Kingdom", "2018-03-14", "Undetermined", "Embryo", "Blood", "Hematopoietic System"], [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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing", "ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 7", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "NextSeq 500", null, "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, null, null, 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", null, "United Kingdom", "2018-03-14", "Undetermined", "Embryo", "Blood", "Hematopoietic System"], [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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing", "ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 6", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "NextSeq 500", null, "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, null, null, 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", null, "United Kingdom", "2018-03-14", "Undetermined", "Embryo", "Blood", "Hematopoietic System"], [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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing", "ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 5", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "NextSeq 500", null, "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, null, null, 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", null, "United Kingdom", "2018-03-14", "Undetermined", "Embryo", "Blood", "Hematopoietic System"], [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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing", "ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 4", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "NextSeq 500", null, "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, null, null, 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", null, "United Kingdom", "2018-03-14", "Undetermined", "Embryo", "Blood", "Hematopoietic System"], [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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing", "ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 3", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "NextSeq 500", null, "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, null, null, 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", null, "United Kingdom", "2018-03-14", "Undetermined", "Embryo", "Blood", "Hematopoietic System"], [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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing", "ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 2", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "NextSeq 500", null, "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, null, null, 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", null, "United Kingdom", "2018-03-14", "Undetermined", "Embryo", "Blood", "Hematopoietic System"], [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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing", "ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 1", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "NextSeq 500", null, "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, null, null, 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", null, "United Kingdom", "2018-03-14", "Undetermined", "Embryo", "Blood", "Hematopoietic System"], [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.", null, "pubmed:28382966", null, "Sample 15 05316 MCK mut3", "GSM7678168", null, "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\u2019d 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", null, "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.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP453114", null, null, "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, null, null, 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", null, "Australia", "2023-08-03", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [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.", null, "pubmed:28382966", null, "Sample 15 05316 MCK mut2", "GSM7678167", null, "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\u2019d 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", null, "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.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP453114", null, null, "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, null, null, 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", null, "Australia", "2023-08-03", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [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.", null, "pubmed:28382966", null, "Sample 15 05316 MCK mut1", "GSM7678166", null, "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\u2019d 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", null, "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.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP453114", null, null, "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, null, null, 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", null, "Australia", "2023-08-03", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [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.", null, "pubmed:28382966", null, "Sample 15 05315 MCK WT3", "GSM7678165", null, "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\u2019d 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", null, "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.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP453114", null, null, "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, null, null, 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", null, "Australia", "2023-08-03", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [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.", null, "pubmed:28382966", null, "Sample 15 05314 MCK WT2", "GSM7678164", null, "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\u2019d 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", null, "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.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP453114", null, null, "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, null, null, 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", null, "Australia", "2023-08-03", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [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.", null, "pubmed:28382966", null, "Sample 15 05313 MCK WT1", "GSM7678163", null, "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\u2019d 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", null, "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.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 1500", null, "SRP453114", null, null, "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, null, null, 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", null, "Australia", "2023-08-03", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [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.", null, null, null, "RNA seq Erythrocytes miR 144 embryo", "miR 144 embryo", null, "isolate:miR 144 mutant|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457465", null, null, "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, null, null, null, 159186558, 130452893, 155820002, 181676510, 60173834, "SRX21515634", "SRS18742881", "SRA1701831", "University of East Anglia|Biological Sciences", "University of East Anglia", 1, 0.52966, null, 0.16941, null, 0.97615, null, 0.58418, null, 61, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-08-30", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [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.", null, null, null, "RNA seq Erythrocytes miR 144 embryo", "miR 144 embryo", null, "isolate:miR 144 mutant|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457465", null, null, "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, null, null, null, 110392869, 106378418, 128881687, 107956679, 41709078, "SRX21515633", "SRS18742881", "SRA1701831", "University of East Anglia|Biological Sciences", "University of East Anglia", 1, 0.32147, null, 0.04496, null, 0.97569, null, 0.58512, null, 31, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-08-30", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [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.", null, null, null, "RNA seq Erythrocytes miR 144 embryo", "miR 144 embryo", null, "isolate:miR 144 mutant|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457465", null, null, "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, null, null, null, 233861010, 192987350, 215192262, 269960344, 62853134, "SRX21515632", "SRS18742881", "SRA1701831", "University of East Anglia|Biological Sciences", "University of East Anglia", 1, 0.77953, null, 0.18084, null, 0.90905, null, 0.74157, null, 75, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-08-30", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [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.", null, null, null, "RNA seq Erythrocytes Wild type embryo", "WT embryo", null, "isolate:Wildtype|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457465", null, null, "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, null, null, null, 154495614, 122942896, 147719345, 179403193, 52578068, "SRX21515631", "SRS18742879", "SRA1701831", "University of East Anglia|Biological Sciences", "University of East Anglia", 1, 0.56358, null, 0.19381, null, 0.96757, null, 0.6115, null, 76, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-08-30", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [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.", null, null, null, "RNA seq Erythrocytes Wild type embryo", "WT embryo", null, "isolate:Wildtype|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457465", null, null, "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, null, null, null, 43225839, 41823862, 54150092, 43159724, 68598492, "SRX21515628", "SRS18742879", "SRA1701831", "University of East Anglia|Biological Sciences", "University of East Anglia", 1, 0.34114, null, 0.05466, null, 0.96664, null, 0.54625, null, 47, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-08-30", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [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.", null, null, null, "RNA seq Erythrocytes Wild type embryo", "WT embryo", null, "isolate:Wildtype|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457465", null, null, "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, null, null, null, 187091550, 151287428, 179967901, 221475884, 76695801, "SRX21515627", "SRS18742879", "SRA1701831", "University of East Anglia|Biological Sciences", "University of East Anglia", 1, 0.61681, null, 0.1874, null, 0.95101, null, 0.56879, null, 29, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "United Kingdom", "2023-08-30", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [30018, "SRR27988043", "SRX23641260", "SRS20476222", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.", null, null, null, "hamp / 36 hpf blood", "zebrafish hamp / 36 hpf blood replicate 3", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:hamp knockdown|sample type:tissue sample|treatment:replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq hamp / 36 hpf blood replicate 3", "B 6", "B 6", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "KO-3_R2_001.fastq.gz KO-3_R1_001.fastq.gz", "fastq fastq", 8752665900.0, 29175553.0, "KO 3 R1 001.fastq.gz", "0:150 1:150", "A:2204170575;C:2174083961;G:2224694970;T:2149603712;N:112682", 150, 150, null, null, 2204170575, 2174083961, 2224694970, 2149603712, 112682, "SRX23641260", "SRS20476222", "SRA1803422", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.91553, 0.91645, 0.01276, 0.01288, 0.85884, 0.85839, 0.35101, 0.40996, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-02-16", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [30019, "SRR27988044", "SRX23641259", "SRS20476221", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.", null, null, null, "hamp / 36 hpf blood", "zebrafish hamp / 36 hpf blood replicate 2", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:hamp knockdown|sample type:tissue sample|treatment:replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq hamp / 36 hpf blood replicate 2", "B 5", "B 5", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "KO-2_R1_001.fastq.gz KO-2_R2_001.fastq.gz", "fastq fastq", 8060498700.0, 26868329.0, "KO 2 R1 001.fastq.gz", "0:150 1:150", "A:2045797336;C:1985847523;G:2035528018;T:1993222840;N:102983", 150, 150, null, null, 2045797336, 1985847523, 2035528018, 1993222840, 102983, "SRX23641259", "SRS20476221", "SRA1803422", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.9213, 0.92027, 0.0167, 0.01676, 0.8242, 0.82475, 0.41081, 0.41111, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-02-16", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [30020, "SRR27988045", "SRX23641258", "SRS20476220", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.", null, null, null, "hamp / 36 hpf blood", "zebrafish hamp / 36 hpf blood replicate 1", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:hamp knockdown|sample type:tissue sample|treatment:replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq hamp / 36 hpf blood replicate 1", "B 4", "B 4", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "KO-1_R1_001.fastq.gz KO-1_R2_001.fastq.gz", "fastq fastq", 8707637700.0, 29025459.0, "KO 1 R1 001.fastq.gz", "0:150 1:150", "A:2222026435;C:2133480283;G:2182087972;T:2169932447;N:110563", 150, 150, null, null, 2222026435, 2133480283, 2182087972, 2169932447, 110563, "SRX23641258", "SRS20476220", "SRA1803422", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.91531, 0.91359, 0.02185, 0.0221, 0.81213, 0.8128, 0.37868, 0.42351, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-02-16", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [30021, "SRR27988046", "SRX23641257", "SRS20476219", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.", null, null, null, "wild type 36 hpf blood", "zebrafish wild type 36 hpf blood replicate 3", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:wild type|sample type:tissue sample|treatment:replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq wild type 36 hpf blood replicate 3", "B 3", "B 3", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "WT-3_R1_001.fastq.gz WT-3_R2_001.fastq.gz", "fastq fastq", 8829371400.0, 29431238.0, "WT 3 R1 001.fastq.gz", "0:150 1:150", "A:2278837675;C:2141723937;G:2193442375;T:2215253519;N:113894", 150, 150, null, null, 2278837675, 2141723937, 2193442375, 2215253519, 113894, "SRX23641257", "SRS20476219", "SRA1803422", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.90531, 0.9043, 0.03015, 0.03017, 0.8101, 0.8112, 0.43085, 0.43002, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-02-16", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [30022, "SRR27988047", "SRX23641256", "SRS20476218", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.", null, null, null, "wild type 36 hpf blood", "zebrafish wild type 36 hpf blood replicate 2", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:wild type|sample type:tissue sample|treatment:replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq wild type 36 hpf blood replicate 2", "B 2", "B 2", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "WT-2_R1_001.fastq.gz WT-2_R2_001.fastq.gz", "fastq fastq", 7365643800.0, 24552146.0, "WT 2 R1 001.fastq.gz", "0:150 1:150", "A:1867985067;C:1819016430;G:1870006707;T:1808540769;N:94827", 150, 150, null, null, 1867985067, 1819016430, 1870006707, 1808540769, 94827, "SRX23641256", "SRS20476218", "SRA1803422", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.90612, 0.90536, 0.01714, 0.01746, 0.88109, 0.88156, 0.32469, 0.39232, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-02-16", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [30023, "SRR27988048", "SRX23641255", "SRS20476217", "SRP485064", "PRJNA1067370", "zebrafish embryo for scRNA seq and bulk RNA seq", "PRJNA1067370", "Other", "Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development accompanied by ferroptosis.", null, null, null, "wild type 36 hpf blood", "zebrafish wild type 36 hpf blood replicate 1", null, "strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:wild type|sample type:tissue sample|treatment:replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq wild type 36 hpf blood replicate 1", "B 1", "B 1", "bulk RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "WT-1_R1_001.fastq.gz WT-1_R2_001.fastq.gz", "fastq fastq", 8631863400.0, 28772878.0, "WT 1 R1 001.fastq.gz", "0:150 1:150", "A:2186212554;C:2135990723;G:2179142081;T:2130408485;N:109557", 150, 150, null, null, 2186212554, 2135990723, 2179142081, 2130408485, 109557, "SRX23641255", "SRS20476217", "SRA1803422", "Shanghai Ocean University|College of Fisheries and Life", "Shanghai Ocean University", 2, 0.90461, 0.90281, 0.01388, 0.01365, 0.83871, 0.83895, 0.36511, 0.41074, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "bulk", "bulk", null, "China", "2024-02-16", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [51876, "SRR8922974", "SRX5704273", "SRS4643334", "SRP192854", "PRJNA533283", "RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish", "GSE129952", "Transcriptome Analysis", "The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.", null, null, null, "erythroid cells: WT6", "GSM3728533", null, "tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type", "erythroid cells: WT6", "basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample", "erythroid cells", null, "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", null, "age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type", "GSM3728533", "GSM3728533: erythroid cells: WT6; Danio rerio; RNA Seq", "GSM3728533", null, "1", "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", "GEO Accession:GSM3728533", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP192854", null, null, "J633_AHFHNLBGX2_TAGCTT_LWT6.1_val_1.fq.gz J633_AHFHNLBGX2_TAGCTT_LWT6.2_val_2.fq.gz", "fastq fastq", 8611605345.0, 32335443.0, "GSM3728533 r1", "0:133.59 1:132.74", "A:1724489451;C:2542199793;G:2626828499;T:1716562999;N:1524603", 133, 132, null, null, 1724489451, 2542199793, 2626828499, 1716562999, 1524603, "SRX5704273", "SRS4643334", "SRA875634", "GEO", "Albert Einstein College of Medicine", 2, 0.91241, 0.96131, 0.10384, 0.10826, 0.77761, 0.7767, 0.69985, 0.69519, 128, 128, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "smarter", "bulk", "unknown", "unknown", null, "United States", "2019-04-17", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [51877, "SRR8922973", "SRX5704272", "SRS4643333", "SRP192854", "PRJNA533283", "RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish", "GSE129952", "Transcriptome Analysis", "The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.", null, null, null, "erythroid cells: WT5", "GSM3728532", null, "tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type", "erythroid cells: WT5", "basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample", "erythroid cells", null, "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", null, "age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type", "GSM3728532", "GSM3728532: erythroid cells: WT5; Danio rerio; RNA Seq", "GSM3728532", null, "1", "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", "GEO Accession:GSM3728532", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP192854", null, null, "J633_AHFHNLBGX2_TGACCA_LWT5.1_val_1.fq.gz J633_AHFHNLBGX2_TGACCA_LWT5.2_val_2.fq.gz", "fastq fastq", 8110446942.0, 28906836.0, "GSM3728532 r1", "0:140.70 1:139.87", "A:1479901358;C:2533764326;G:2613647627;T:1481710129;N:1423502", 140, 139, null, null, 1479901358, 2533764326, 2613647627, 1481710129, 1423502, "SRX5704272", "SRS4643333", "SRA875634", "GEO", "Albert Einstein College of Medicine", 2, 0.92578, 0.97511, 0.09182, 0.09201, 0.80503, 0.80324, 0.76985, 0.7675, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "smarter", "bulk", "unknown", "unknown", null, "United States", "2019-04-17", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [51878, "SRR8922972", "SRX5704271", "SRS4643332", "SRP192854", "PRJNA533283", "RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish", "GSE129952", "Transcriptome Analysis", "The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.", null, null, null, "erythroid cells: WT4", "GSM3728531", null, "tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type", "erythroid cells: WT4", "basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample", "erythroid cells", null, "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", null, "age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type", "GSM3728531", "GSM3728531: erythroid cells: WT4; Danio rerio; RNA Seq", "GSM3728531", null, "1", "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", "GEO Accession:GSM3728531", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP192854", null, null, "J633_AHFHNLBGX2_TTAGGC_LWT4.2_val_2.fq.gz J633_AHFHNLBGX2_TTAGGC_LWT4.1_val_1.fq.gz", "fastq fastq", 8627466135.0, 32957109.0, "GSM3728531 r1", "0:131.12 1:130.66", "A:1686521982;C:2592728511;G:2670950174;T:1675745501;N:1519967", 131, 130, null, null, 1686521982, 2592728511, 2670950174, 1675745501, 1519967, "SRX5704271", "SRS4643332", "SRA875634", "GEO", "Albert Einstein College of Medicine", 2, 0.91773, 0.96731, 0.11151, 0.1134, 0.78792, 0.78597, 0.73657, 0.73692, 104, 104, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "smarter", "bulk", "unknown", "unknown", null, "United States", "2019-04-17", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [51879, "SRR8922971", "SRX5704270", "SRS4643331", "SRP192854", "PRJNA533283", "RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish", "GSE129952", "Transcriptome Analysis", "The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.", null, null, null, "erythroid cells: WT3", "GSM3728530", null, "tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type", "erythroid cells: WT3", "basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample", "erythroid cells", null, "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", null, "age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type", "GSM3728530", "GSM3728530: erythroid cells: WT3; Danio rerio; RNA Seq", "GSM3728530", null, "1", "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", "GEO Accession:GSM3728530", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP192854", null, null, "J633_AHFHNLBGX2_CGATGT_LWT3.2_val_2.fq.gz J633_AHFHNLBGX2_CGATGT_LWT3.1_val_1.fq.gz", "fastq fastq", 7675701402.0, 28099783.0, "GSM3728530 r1", "0:136.90 1:136.26", "A:1496106079;C:2307580110;G:2386093773;T:1484556287;N:1365153", 136, 136, null, null, 1496106079, 2307580110, 2386093773, 1484556287, 1365153, "SRX5704270", "SRS4643331", "SRA875634", "GEO", "Albert Einstein College of Medicine", 2, 0.91833, 0.96754, 0.10771, 0.10822, 0.80135, 0.80158, 0.76757, 0.7524, 150, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "smarter", "bulk", "unknown", "unknown", null, "United States", "2019-04-17", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [51880, "SRR8922970", "SRX5704269", "SRS4643330", "SRP192854", "PRJNA533283", "RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish", "GSE129952", "Transcriptome Analysis", "The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.", null, null, null, "erythroid cells: WT2", "GSM3728529", null, "tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant", "erythroid cells: WT2", "basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample", "erythroid cells", null, "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", null, "age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant", "GSM3728529", "GSM3728529: erythroid cells: WT2; Danio rerio; RNA Seq", "GSM3728529", null, "1", "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", "GEO Accession:GSM3728529", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP192854", null, null, "J633_AHFHNLBGX2_ATCACG_LWT2.2_val_2.fq.gz J633_AHFHNLBGX2_ATCACG_LWT2.1_val_1.fq.gz", "fastq fastq", 8749226933.0, 32236600.0, "GSM3728529 r1", "0:135.97 1:135.43", "A:1818348438;C:2523018672;G:2595068272;T:1811215171;N:1576380", 135, 135, null, null, 1818348438, 2523018672, 2595068272, 1811215171, 1576380, "SRX5704269", "SRS4643330", "SRA875634", "GEO", "Albert Einstein College of Medicine", 2, 0.91533, 0.96543, 0.12825, 0.13005, 0.77394, 0.77344, 0.70772, 0.67993, 143, 143, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "smarter", "bulk", "unknown", "unknown", null, "United States", "2019-04-17", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [51881, "SRR8922969", "SRX5704268", "SRS4643329", "SRP192854", "PRJNA533283", "RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish", "GSE129952", "Transcriptome Analysis", "The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.", null, null, null, "erythroid cells: Mut6", "GSM3728528", null, "tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant", "erythroid cells: Mut6", "basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample", "erythroid cells", null, "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", null, "age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant", "GSM3728528", "GSM3728528: erythroid cells: Mut6; Danio rerio; RNA Seq", "GSM3728528", null, "1", "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", "GEO Accession:GSM3728528", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP192854", null, null, "J633_AHFHNLBGX2_GGCTAC_LMut6.2_val_2.fq.gz J633_AHFHNLBGX2_GGCTAC_LMut6.1_val_1.fq.gz", "fastq fastq", 7989745578.0, 29813232.0, "GSM3728528 r1", "0:134.59 1:133.41", "A:1487912329;C:2465671654;G:2552013900;T:1482837472;N:1310223", 134, 133, null, null, 1487912329, 2465671654, 2552013900, 1482837472, 1310223, "SRX5704268", "SRS4643329", "SRA875634", "GEO", "Albert Einstein College of Medicine", 2, 0.91636, 0.96506, 0.12513, 0.13214, 0.80255, 0.80277, 0.77309, 0.77779, 106, 106, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "smarter", "bulk", "unknown", "unknown", null, "United States", "2019-04-17", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [51882, "SRR8922968", "SRX5704267", "SRS4643327", "SRP192854", "PRJNA533283", "RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish", "GSE129952", "Transcriptome Analysis", "The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.", null, null, null, "erythroid cells: Mut5", "GSM3728527", null, "tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant", "erythroid cells: Mut5", "basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample", "erythroid cells", null, "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", null, "age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant", "GSM3728527", "GSM3728527: erythroid cells: Mut5; Danio rerio; RNA Seq", "GSM3728527", null, "1", "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", "GEO Accession:GSM3728527", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP192854", null, null, "J633_AHFHNLBGX2_GATCAG_LMut5.2_val_2.fq.gz J633_AHFHNLBGX2_GATCAG_LMut5.1_val_1.fq.gz", "fastq fastq", 8500296799.0, 30812271.0, "GSM3728527 r1", "0:138.28 1:137.59", "A:1566669253;C:2640866820;G:2726747970;T:1564531299;N:1481457", 138, 137, null, null, 1566669253, 2640866820, 2726747970, 1564531299, 1481457, "SRX5704267", "SRS4643327", "SRA875634", "GEO", "Albert Einstein College of Medicine", 2, 0.91987, 0.9688, 0.10388, 0.10646, 0.80338, 0.80176, 0.75914, 0.71799, 52, 52, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "smarter", "bulk", "unknown", "unknown", null, "United States", "2019-04-17", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [51883, "SRR8922967", "SRX5704266", "SRS4643328", "SRP192854", "PRJNA533283", "RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish", "GSE129952", "Transcriptome Analysis", "The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.", null, null, null, "erythroid cells: Mut4", "GSM3728526", null, "tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant", "erythroid cells: Mut4", "basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample", "erythroid cells", null, "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", null, "age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant", "GSM3728526", "GSM3728526: erythroid cells: Mut4; Danio rerio; RNA Seq", "GSM3728526", null, "1", "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", "GEO Accession:GSM3728526", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP192854", null, null, "J633_AHFHNLBGX2_ACTTGA_LMut4.2_val_2.fq.gz J633_AHFHNLBGX2_ACTTGA_LMut4.1_val_1.fq.gz", "fastq fastq", 8415322795.0, 32199684.0, "GSM3728526 r1", "0:130.80 1:130.55", "A:1593557159;C:2583771193;G:2657553064;T:1578891748;N:1549631", 130, 130, null, null, 1593557159, 2583771193, 2657553064, 1578891748, 1549631, "SRX5704266", "SRS4643328", "SRA875634", "GEO", "Albert Einstein College of Medicine", 2, 0.92078, 0.97122, 0.12063, 0.12061, 0.81994, 0.81822, 0.76635, 0.7826, 149, 148, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "smarter", "bulk", "unknown", "unknown", null, "United States", "2019-04-17", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [51884, "SRR8922966", "SRX5704265", "SRS4643326", "SRP192854", "PRJNA533283", "RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish", "GSE129952", "Transcriptome Analysis", "The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.", null, null, null, "erythroid cells: Mut3", "GSM3728525", null, "tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant", "erythroid cells: Mut3", "basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample", "erythroid cells", null, "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", null, "age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant", "GSM3728525", "GSM3728525: erythroid cells: Mut3; Danio rerio; RNA Seq", "GSM3728525", null, "1", "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", "GEO Accession:GSM3728525", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP192854", null, null, "J633_AHFHNLBGX2_CAGATC_LMut3.2_val_2.fq.gz J633_AHFHNLBGX2_CAGATC_LMut3.1_val_1.fq.gz", "fastq fastq", 5373096143.0, 19350806.0, "GSM3728525 r1", "0:139.04 1:138.63", "A:990313321;C:1667762750;G:1723819167;T:990236765;N:964140", 139, 138, null, null, 990313321, 1667762750, 1723819167, 990236765, 964140, "SRX5704265", "SRS4643326", "SRA875634", "GEO", "Albert Einstein College of Medicine", 2, 0.92305, 0.97223, 0.10386, 0.10158, 0.8062, 0.80415, 0.79641, 0.78792, 150, 149, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "smarter", "bulk", "unknown", "unknown", null, "United States", "2019-04-17", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [51885, "SRR8922965", "SRX5704264", "SRS4643325", "SRP192854", "PRJNA533283", "RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish", "GSE129952", "Transcriptome Analysis", "The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.", null, null, null, "erythroid cells: Mut1", "GSM3728524", null, "tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant", "erythroid cells: Mut1", "basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample", "erythroid cells", null, "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", null, "age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant", "GSM3728524", "GSM3728524: erythroid cells: Mut1; Danio rerio; RNA Seq", "GSM3728524", null, "1", "Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.", "GEO Accession:GSM3728524", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP192854", null, null, "J633_AHFHNLBGX2_GCCAAT_LMut1.1_val_1.fq.gz J633_AHFHNLBGX2_GCCAAT_LMut1.2_val_2.fq.gz", "fastq fastq", 7256147960.0, 27513744.0, "GSM3728524 r1", "0:132.21 1:131.52", "A:1506751800;C:2097058291;G:2163719918;T:1487337753;N:1280198", 132, 131, null, null, 1506751800, 2097058291, 2163719918, 1487337753, 1280198, "SRX5704264", "SRS4643325", "SRA875634", "GEO", "Albert Einstein College of Medicine", 2, 0.90512, 0.95369, 0.12564, 0.13165, 0.77153, 0.77098, 0.74915, 0.74717, 122, 122, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "rrna_depletion", "smarter", "bulk", "unknown", "unknown", null, "United States", "2019-04-17", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [53001, "SRR12173589", "SRX8688333", "SRS6966994", "SRP213938", "PRJNA553572", "A map of cis regulatory elements and 3D genome structures in zebrafish", "GSE134055", "Other", "The zebrafish has been widely used for the study of human disease and development as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome however has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects we performed RNA seq ATAC seq ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall we have identified 235 596 cis regulatory elements which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish human and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore through the analysis of Hi C data in zebrafish brain and muscle we observed different levels of 3D genome organization including compartment topological associating domains TADs and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3 RNA Seq 11 of them were examined using ATAC seq WGBS and ChIP seq H3K9me3 and H3K9me2 and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that for the samples GSM4661977 GSM4662088 [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.", null, "pubmed:33239788;pubmed:35649578", null, "YueLab RNA seq Blood rep2", "GSM4662086", null, "source name:YueLab RNA seq Blood|strain:Tuebingen|tissue:Blood", "YueLab RNA seq Blood rep2", "RNA seq reads were aligned to zv10 genome assembly using STAR; The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using Bowtie2;H3K27ac H3K4me3 ChIP seq were called using MACS2 with the following setting: ChIP seq q value <10e 2 p value<10e 5 Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5.For the ATAC seq the peak length were fixed to 500 bp. We only selected the peak with the most significant signal if several peaks overlap with each other in each tissue.Since the H3K9me3 and H3K9me2 makers are broad domain we called the peak using Homer with the parameter \u201c region size 1000\u201d and peaks within 5 kb were merged together. HiC matrix was generated using HiC Pro WGBS data were mapped to in silico bisulfite converted zebrafish genome reference by using Bismark For the scATAC seq the BCL files generated from sequencing were used as inputs to the 10X Genomics Cell Ranger ATAC seq pipeline; then the FASTQ files were aligned to the GRCz10 genome using BWA and the fragments with MAPQ>30 were kept for further analysis and each fragment is associated with a single cell barcode. Genome build: zv10GRCz10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged", "YueLab RNA seq Blood", null, "RNA seq: For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol\u00ae according to the protocol Invitrogen. RNA seq: The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer\u2019s protocol. Briefly polyA RNA was purified from 1000\u00a0ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. ChIP seq: All the tissues were ground in the liquid nitrogen and fixed by 1% formaldehyde at room temperature for 15 min. 0.2 M glycine was added and incubated at room temperature for 5 min to quench the fixation. Fixed tissues were then washed once by cold 1X PBS. Tissue pellet was resuspended and incubated on ice for 10 min in 100 \u00b5L of ChIP seq lysis buffer 20 mM Tris HCl pH 8.0 1% SDS 50 mM EDTA 1X proteinase inhibitor cocktail. Next 900 \u00b5L cold 1X TE buffer was added to dilute SDS concentration and the nuclei suspension was sonicated using Covaris E220 with the following parameters: 140 W duty factor 5 200 per burst. Sonication time is variable depending on tissue types. To check the chromatin fragmentation size 20 \u00b5L of input chromatin was reverse crosslinked in elution buffer 20 mM Tris HCl pH 8.0 1% SDS 1 mM EDTA at 65 \u00b0C overnight treated with Rnase A and proteinase K and purified by phenol chloroform extraction. Input DNA was then loaded on a Lonza flash gel to make sure that the majority of DNA size distributes between 100 300 bp. To prepare antibody beads complex 3 \u00b5g of histone H3K27ac antibody Active Motif 39133 or H3K4me3 antibody EMD Millipore 07 473 was mix with 12 \u00b5L M 280 sheep anti rabbit IgG Dynabeads ThermoFisher 11203D in 150 \u00b5L of 5 mg/mL BSA/1X PBS buffer with rotation at 4 \u00b0C for 3 h. post incubation antibody beads complex was washed once with BSA/1X PBS buffer. About 200 \u00b5g chromatin was used per IP. Equal volume of master mix 1X TE 2% Triton X 100 0.2% sodium deoxycholate 2X proteinase inhibitor cocktail was mixed with 200 \u00b5g chromatin and then incubated with antibody beads complex overnight with rotation. The next morning the beads were washed 5 times with cold RIPA wash buffer 20 mM Tris HCl pH 8.0 1% NP 40 0.7% sodium deoxycholate 500 mM LiCl 1 mM EDTA 1X proteinase inhibitor cocktail. Then the chromatin bound on the beads was eluted by 150 \u00b5L of elution buffer at 65 \u00b0C for 30 min. ChIP seq: To prepare the library eluted chromatin was reverse crosslinked and purified by phenol chloroform extraction. Then DNA was end repaired by END IT DNA end repair kit Epicentre ER81050 according to kit\u2019s protocol added A using Klenow fragment 3\u2019 >5\u2019 exo NEB M0212S ligated with Illumina TruSeq adaptor Illumina FC 121 3001 and subsequently amplified by PCR Roche kk2601. The quality and quantity of all the libraries were checked using BioAnalyzer High Sensitivity DNA Kit Agilent. The libraries were sequenced on Illumina HiSeq 2500 with reads length of 2X 50 bp or 2X 100 bp. ATAC seq: Tuebingen adult tissues were ground in liquid nitrogen resuspended in 1 mL of lysis buffer 1X PBS 0.2% NP 40 5% BSA 1 mM DTT protease inhibitors followed by incubation at 4 \u00b0C for 10 min on an overhead shaker. post that lysate was filtered through 40 \uf06dm cell strainer and nuclei were collected at 1000X g for 5 min. ATAC seq: Tagmentation was performed immediately according to ATAC seq protocol reported previouslyBuenrostro et al. 2013 Hi C: For brain tissue two adult Tuebingen brains were slightly ground into small granules in liquid nitrogen and resuspended in 1 mL of cold hypotonic buffer 20 mM Tris HCl pH 8.0 10 mM NaCl 20 mM EDTA. Granular brains were then dounce homogenized with loose pestle for 20 times. The top of the homogenate was carefully transferred into a new tube and fixed with 2% formaldehyde at room temperature for 10 min. 0.2 M of glycine was added to stop fixation. For muscle tissue 60 mg of Tuebingen muscle was first chopped into small pieces and digested by 0.25% trypsin at room temperature for 30 min. post neutralization with FBS muscle cells were resuspended in cold 1X PBS and fixed with 2% of formaldehyde at room temperature for 10 min. 0.2 M glycine was then added to stop fixation. Hi C: Hi C experiments on adult zebrafish brain and muscle tissues were performed according to previously published protocolRao et al. 2014. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 100 bp high throughput sequencing using HiSeq 2500 or HiSeq 4000Illumina. WGBS: T\u00fcbingen adult tissues were dissected and the genomic DNA was extracted using DNeasy Blood & Tissue Kit Qiagen 69504. Then 1 \u00b5g of genomic DNA of each adult tissue was subjected to bisulfite conversion using EZ DNA Methylation Gold Kits WGBS: The final libraries were prepared using the Accel NGS\u00ae Methyl Seq DNA Library Kit. scATAC seq: Single cell ATAC seq scATAC seq was performed in one female brain and one male brain respectively on the 10X Genomics platform. To isolate nuclei freshly dissected single brain was transferred to 1 mL NbActiv1 medium BrainBits NbActiv1 500 with a wide bore pipette tip to break the tissue into small pieces. Then the tissue was broken up completely using regular bore pipette tips followed by filtering through a 30 \u00b5m cell strainer. The isolated cells were spun down at 500 g for 5 min at 4 \u00b0C and then lysed in 100 \u00b5L chilled 0.1X Lysis Buffer 10 mM Tris HCl pH 7.5 10 mM NaCl 3 mM MgCl2 1% BSA 0.01% Tween 20 0.01% NP40 and 0.001% digitonin on ice for 5 min. Then 1 mL chilled Wash Buffer 10 mM Tris HCl pH 7.5 10 mM NaCl 3 mM MgCl2 1% BSA 0.1% Tween 20 was added to the lysed cells and cells were spun down at 500 g for 5 min at 4 \u00b0C. At last 300 \u00b5L chilled Diluted Nuclei Buffer 10x Genomics PN 2000153/2000207 was added to resuspend the nuclei. The nuclei were filtered again using a 30 \u00b5m cell strainer before cell counting scATAC seq: Around 12 000 nuclei were used for one Tn5 tagmentation reaction and the scATAC seq library was prepared and sequenced exactly according to the company\u2019s user guide.", "RNA seq: Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions ChIP seq ATAC seq Hi C and WGBS: Ault Tuebingen zebrafish were raised under standard laboratory conditions", "strain:Tuebingen|tissue:Blood", "GSM4662086", "GSM4662086: YueLab RNA seq Blood rep2; Danio rerio; RNA Seq", "GSM4662086", null, "1", "RNA seq: For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol\u00ae according to the protocol Invitrogen. RNA seq: The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. ChIP seq: All the tissues were ground in the liquid nitrogen and fixed by 1% formaldehyde at room temperature for 15 min. 0.2 M glycine was added and incubated at room temperature for 5 min to quench the fixation. Fixed tissues were then washed once by cold 1X PBS. Tissue pellet was resuspended and incubated on ice for 10 min in 100 \u00b5L of ChIP seq lysis buffer 20 mM Tris HCl pH 8.0 1% SDS 50 mM EDTA 1X proteinase inhibitor cocktail. Next 900 \u00b5L cold 1X TE buffer was added to dilute SDS concentration and the nuclei suspension was sonicated using Covaris E220 with the following parameters: 140 W duty factor 5 200 per burst. Sonication time is variable depending on tissue types. To check the chromatin fragmentation size 20 \u00b5L of input chromatin was reverse crosslinked in elution buffer 20 mM Tris HCl pH 8.0 1% SDS 1 mM EDTA at 65 \u00b0C overnight treated with Rnase A and proteinase K and purified by phenol chloroform extraction. Input DNA was then loaded on a Lonza flash gel to make sure that the majority of DNA size distributes between 100 300 bp. To prepare antibody beads complex 3 \u00b5g of histone H3K27ac antibody Active Motif 39133 or H3K4me3 antibody EMD Millipore 07 473 was mix with 12 \u00b5L M 280 sheep anti rabbit IgG Dynabeads ThermoFisher 11203D in 150 \u00b5L of 5 mg/mL BSA/1X PBS buffer with rotation at 4 \u00b0C for 3 h. post incubation antibody beads complex was washed once with BSA/1X PBS buffer. About 200 \u00b5g chromatin was used per IP. Equal volume of master mix 1X TE 2% Triton X 100 0.2% sodium deoxycholate 2X proteinase inhibitor cocktail was mixed with 200 \u00b5g chromatin and then incubated with antibody beads complex overnight with rotation. The next morning the beads were washed 5 times with cold RIPA wash buffer 20 mM Tris HCl pH 8.0 1% NP 40 0.7% sodium deoxycholate 500 mM LiCl 1 mM EDTA 1X proteinase inhibitor cocktail. Then the chromatin bound on the beads was eluted by 150 \u00b5L of elution buffer at 65 \u00b0C for 30 min. ChIP seq: To prepare the library eluted chromatin was reverse crosslinked and purified by phenol chloroform extraction. Then DNA was end repaired by END IT DNA end repair kit Epicentre ER81050 according to kit's protocol added A using Klenow fragment three prime >five prime exo NEB M0212S ligated with Illumina TruSeq adaptor Illumina FC 121 3001 and subsequently amplified by PCR Roche kk2601. The quality and quantity of all the libraries were checked using BioAnalyzer High Sensitivity DNA Kit Agilent. The libraries were sequenced on Illumina HiSeq 2500 with reads length of 2X 50 bp or 2X 100 bp. ATAC seq: Tuebingen adult tissues were ground in liquid nitrogen resuspended in 1 mL of lysis buffer 1X PBS 0.2% NP 40 5% BSA 1 mM DTT protease inhibitors followed by incubation at 4 \u00b0C for 10 min on an overhead shaker. post that lysate was filtered through 40 \uf06dm cell strainer and nuclei were collected at 1000X g for 5 min. ATAC seq: Tagmentation was performed immediately according to ATAC seq protocol reported previouslyBuenrostro et al. 2013 Hi C: For brain tissue two adult Tuebingen brains were slightly ground into small granules in liquid nitrogen and resuspended in 1 mL of cold hypotonic buffer 20 mM Tris HCl pH 8.0 10 mM NaCl 20 mM EDTA. Granular brains were then dounce homogenized with loose pestle for 20 times. The top of the homogenate was carefully transferred into a new tube and fixed with 2% formaldehyde at room temperature for 10 min. 0.2 M of glycine was added to stop fixation. For muscle tissue 60 mg of Tuebingen muscle was first chopped into small pieces and digested by 0.25% trypsin at room temperature for 30 min. post neutralization with FBS muscle cells were resuspended in cold 1X PBS and fixed with 2% of formaldehyde at room temperature for 10 min. 0.2 M glycine was then added to stop fixation. Hi C: Hi C experiments on adult zebrafish brain and muscle tissues were performed according to previously published protocolRao et al. 2014. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 100 bp high throughput sequencing using HiSeq 2500 or HiSeq 4000Illumina. WGBS: T\u00fcbingen adult tissues were dissected and the genomic DNA was extracted using DNeasy Blood & Tissue Kit Qiagen 69504. Then 1 \u00b5g of genomic DNA of each adult tissue was subjected to bisulfite conversion using EZ DNA Methylation Gold Kits WGBS: The final libraries were prepared using the Accel NGS\u00ae Methyl Seq DNA Library Kit. scATAC seq: Single cell ATAC seq scATAC seq was performed in one female brain and one male brain respectively on the 10X Genomics platform. To isolate nuclei freshly dissected single brain was transferred to 1 mL NbActiv1 medium BrainBits NbActiv1 500 with a wide bore pipette tip to break the tissue into small pieces. Then the tissue was broken up completely using regular bore pipette tips followed by filtering through a 30 \u00b5m cell strainer. The isolated cells were spun down at 500 g for 5 min at 4 \u00b0C and then lysed in 100 \u00b5L chilled 0.1X Lysis Buffer 10 mM Tris HCl pH 7.5 10 mM NaCl 3 mM MgCl2 1% BSA 0.01% Tween 20 0.01% NP40 and 0.001% digitonin on ice for 5 min. Then 1 mL chilled Wash Buffer 10 mM Tris HCl pH 7.5 10 mM NaCl 3 mM MgCl2 1% BSA 0.1% Tween 20 was added to the lysed cells and cells were spun down at 500 g for 5 min at 4 \u00b0C. At last 300 \u00b5L chilled Diluted Nuclei Buffer 10x Genomics PN 2000153/2000207 was added to resuspend the nuclei. The nuclei were filtered again using a 30 \u00b5m cell strainer before cell counting scATAC seq: Around 12 000 nuclei were used for one Tn5 tagmentation reaction and the scATAC seq library was prepared and sequenced exactly according to the company's user guide.", "GEO Accession:GSM4662086", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP213938", null, null, "YueLab-RNA-seq-Blood-rep2_2.fastq.gz YueLab-RNA-seq-Blood-rep2_1.fastq.gz", "fastq fastq", 9750305560.0, 32285780.0, "GSM4662086 r1", "0:151 1:151", "A:2564237490;C:2313022617;G:2328740350;T:2544206938;N:98165", 151, 151, null, null, 2564237490, 2313022617, 2328740350, 2544206938, 98165, "SRX8688333", "SRS6966994", "SRA919194", "GEO", "Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine", 2, 0.90976, 0.90587, 0.07014, 0.06953, 0.85415, 0.85624, 0.51898, 0.51696, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "sc", "single_cell_droplet", "10x", null, "United States", "2020-07-08", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [53002, "SRR12173588", "SRX8688332", "SRS6966993", "SRP213938", "PRJNA553572", "A map of cis regulatory elements and 3D genome structures in zebrafish", "GSE134055", "Other", "The zebrafish has been widely used for the study of human disease and development as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome however has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects we performed RNA seq ATAC seq ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall we have identified 235 596 cis regulatory elements which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish human and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore through the analysis of Hi C data in zebrafish brain and muscle we observed different levels of 3D genome organization including compartment topological associating domains TADs and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3 RNA Seq 11 of them were examined using ATAC seq WGBS and ChIP seq H3K9me3 and H3K9me2 and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that for the samples GSM4661977 GSM4662088 [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.", null, "pubmed:33239788;pubmed:35649578", null, "YueLab RNA seq Blood rep1", "GSM4662085", null, "source name:YueLab RNA seq Blood|strain:Tuebingen|tissue:Blood", "YueLab RNA seq Blood rep1", "RNA seq reads were aligned to zv10 genome assembly using STAR; The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using Bowtie2;H3K27ac H3K4me3 ChIP seq were called using MACS2 with the following setting: ChIP seq q value <10e 2 p value<10e 5 Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5.For the ATAC seq the peak length were fixed to 500 bp. We only selected the peak with the most significant signal if several peaks overlap with each other in each tissue.Since the H3K9me3 and H3K9me2 makers are broad domain we called the peak using Homer with the parameter \u201c region size 1000\u201d and peaks within 5 kb were merged together. HiC matrix was generated using HiC Pro WGBS data were mapped to in silico bisulfite converted zebrafish genome reference by using Bismark For the scATAC seq the BCL files generated from sequencing were used as inputs to the 10X Genomics Cell Ranger ATAC seq pipeline; then the FASTQ files were aligned to the GRCz10 genome using BWA and the fragments with MAPQ>30 were kept for further analysis and each fragment is associated with a single cell barcode. Genome build: zv10GRCz10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged", "YueLab RNA seq Blood", null, "RNA seq: For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol\u00ae according to the protocol Invitrogen. RNA seq: The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer\u2019s protocol. Briefly polyA RNA was purified from 1000\u00a0ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. ChIP seq: All the tissues were ground in the liquid nitrogen and fixed by 1% formaldehyde at room temperature for 15 min. 0.2 M glycine was added and incubated at room temperature for 5 min to quench the fixation. Fixed tissues were then washed once by cold 1X PBS. Tissue pellet was resuspended and incubated on ice for 10 min in 100 \u00b5L of ChIP seq lysis buffer 20 mM Tris HCl pH 8.0 1% SDS 50 mM EDTA 1X proteinase inhibitor cocktail. Next 900 \u00b5L cold 1X TE buffer was added to dilute SDS concentration and the nuclei suspension was sonicated using Covaris E220 with the following parameters: 140 W duty factor 5 200 per burst. Sonication time is variable depending on tissue types. To check the chromatin fragmentation size 20 \u00b5L of input chromatin was reverse crosslinked in elution buffer 20 mM Tris HCl pH 8.0 1% SDS 1 mM EDTA at 65 \u00b0C overnight treated with Rnase A and proteinase K and purified by phenol chloroform extraction. Input DNA was then loaded on a Lonza flash gel to make sure that the majority of DNA size distributes between 100 300 bp. To prepare antibody beads complex 3 \u00b5g of histone H3K27ac antibody Active Motif 39133 or H3K4me3 antibody EMD Millipore 07 473 was mix with 12 \u00b5L M 280 sheep anti rabbit IgG Dynabeads ThermoFisher 11203D in 150 \u00b5L of 5 mg/mL BSA/1X PBS buffer with rotation at 4 \u00b0C for 3 h. post incubation antibody beads complex was washed once with BSA/1X PBS buffer. About 200 \u00b5g chromatin was used per IP. Equal volume of master mix 1X TE 2% Triton X 100 0.2% sodium deoxycholate 2X proteinase inhibitor cocktail was mixed with 200 \u00b5g chromatin and then incubated with antibody beads complex overnight with rotation. The next morning the beads were washed 5 times with cold RIPA wash buffer 20 mM Tris HCl pH 8.0 1% NP 40 0.7% sodium deoxycholate 500 mM LiCl 1 mM EDTA 1X proteinase inhibitor cocktail. Then the chromatin bound on the beads was eluted by 150 \u00b5L of elution buffer at 65 \u00b0C for 30 min. ChIP seq: To prepare the library eluted chromatin was reverse crosslinked and purified by phenol chloroform extraction. Then DNA was end repaired by END IT DNA end repair kit Epicentre ER81050 according to kit\u2019s protocol added A using Klenow fragment 3\u2019 >5\u2019 exo NEB M0212S ligated with Illumina TruSeq adaptor Illumina FC 121 3001 and subsequently amplified by PCR Roche kk2601. The quality and quantity of all the libraries were checked using BioAnalyzer High Sensitivity DNA Kit Agilent. The libraries were sequenced on Illumina HiSeq 2500 with reads length of 2X 50 bp or 2X 100 bp. ATAC seq: Tuebingen adult tissues were ground in liquid nitrogen resuspended in 1 mL of lysis buffer 1X PBS 0.2% NP 40 5% BSA 1 mM DTT protease inhibitors followed by incubation at 4 \u00b0C for 10 min on an overhead shaker. post that lysate was filtered through 40 \uf06dm cell strainer and nuclei were collected at 1000X g for 5 min. ATAC seq: Tagmentation was performed immediately according to ATAC seq protocol reported previouslyBuenrostro et al. 2013 Hi C: For brain tissue two adult Tuebingen brains were slightly ground into small granules in liquid nitrogen and resuspended in 1 mL of cold hypotonic buffer 20 mM Tris HCl pH 8.0 10 mM NaCl 20 mM EDTA. Granular brains were then dounce homogenized with loose pestle for 20 times. The top of the homogenate was carefully transferred into a new tube and fixed with 2% formaldehyde at room temperature for 10 min. 0.2 M of glycine was added to stop fixation. For muscle tissue 60 mg of Tuebingen muscle was first chopped into small pieces and digested by 0.25% trypsin at room temperature for 30 min. post neutralization with FBS muscle cells were resuspended in cold 1X PBS and fixed with 2% of formaldehyde at room temperature for 10 min. 0.2 M glycine was then added to stop fixation. Hi C: Hi C experiments on adult zebrafish brain and muscle tissues were performed according to previously published protocolRao et al. 2014. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 100 bp high throughput sequencing using HiSeq 2500 or HiSeq 4000Illumina. WGBS: T\u00fcbingen adult tissues were dissected and the genomic DNA was extracted using DNeasy Blood & Tissue Kit Qiagen 69504. Then 1 \u00b5g of genomic DNA of each adult tissue was subjected to bisulfite conversion using EZ DNA Methylation Gold Kits WGBS: The final libraries were prepared using the Accel NGS\u00ae Methyl Seq DNA Library Kit. scATAC seq: Single cell ATAC seq scATAC seq was performed in one female brain and one male brain respectively on the 10X Genomics platform. To isolate nuclei freshly dissected single brain was transferred to 1 mL NbActiv1 medium BrainBits NbActiv1 500 with a wide bore pipette tip to break the tissue into small pieces. Then the tissue was broken up completely using regular bore pipette tips followed by filtering through a 30 \u00b5m cell strainer. The isolated cells were spun down at 500 g for 5 min at 4 \u00b0C and then lysed in 100 \u00b5L chilled 0.1X Lysis Buffer 10 mM Tris HCl pH 7.5 10 mM NaCl 3 mM MgCl2 1% BSA 0.01% Tween 20 0.01% NP40 and 0.001% digitonin on ice for 5 min. Then 1 mL chilled Wash Buffer 10 mM Tris HCl pH 7.5 10 mM NaCl 3 mM MgCl2 1% BSA 0.1% Tween 20 was added to the lysed cells and cells were spun down at 500 g for 5 min at 4 \u00b0C. At last 300 \u00b5L chilled Diluted Nuclei Buffer 10x Genomics PN 2000153/2000207 was added to resuspend the nuclei. The nuclei were filtered again using a 30 \u00b5m cell strainer before cell counting scATAC seq: Around 12 000 nuclei were used for one Tn5 tagmentation reaction and the scATAC seq library was prepared and sequenced exactly according to the company\u2019s user guide.", "RNA seq: Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions ChIP seq ATAC seq Hi C and WGBS: Ault Tuebingen zebrafish were raised under standard laboratory conditions", "strain:Tuebingen|tissue:Blood", "GSM4662085", "GSM4662085: YueLab RNA seq Blood rep1; Danio rerio; RNA Seq", "GSM4662085", null, "1", "RNA seq: For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol\u00ae according to the protocol Invitrogen. RNA seq: The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. ChIP seq: All the tissues were ground in the liquid nitrogen and fixed by 1% formaldehyde at room temperature for 15 min. 0.2 M glycine was added and incubated at room temperature for 5 min to quench the fixation. Fixed tissues were then washed once by cold 1X PBS. Tissue pellet was resuspended and incubated on ice for 10 min in 100 \u00b5L of ChIP seq lysis buffer 20 mM Tris HCl pH 8.0 1% SDS 50 mM EDTA 1X proteinase inhibitor cocktail. Next 900 \u00b5L cold 1X TE buffer was added to dilute SDS concentration and the nuclei suspension was sonicated using Covaris E220 with the following parameters: 140 W duty factor 5 200 per burst. Sonication time is variable depending on tissue types. To check the chromatin fragmentation size 20 \u00b5L of input chromatin was reverse crosslinked in elution buffer 20 mM Tris HCl pH 8.0 1% SDS 1 mM EDTA at 65 \u00b0C overnight treated with Rnase A and proteinase K and purified by phenol chloroform extraction. Input DNA was then loaded on a Lonza flash gel to make sure that the majority of DNA size distributes between 100 300 bp. To prepare antibody beads complex 3 \u00b5g of histone H3K27ac antibody Active Motif 39133 or H3K4me3 antibody EMD Millipore 07 473 was mix with 12 \u00b5L M 280 sheep anti rabbit IgG Dynabeads ThermoFisher 11203D in 150 \u00b5L of 5 mg/mL BSA/1X PBS buffer with rotation at 4 \u00b0C for 3 h. post incubation antibody beads complex was washed once with BSA/1X PBS buffer. About 200 \u00b5g chromatin was used per IP. Equal volume of master mix 1X TE 2% Triton X 100 0.2% sodium deoxycholate 2X proteinase inhibitor cocktail was mixed with 200 \u00b5g chromatin and then incubated with antibody beads complex overnight with rotation. The next morning the beads were washed 5 times with cold RIPA wash buffer 20 mM Tris HCl pH 8.0 1% NP 40 0.7% sodium deoxycholate 500 mM LiCl 1 mM EDTA 1X proteinase inhibitor cocktail. Then the chromatin bound on the beads was eluted by 150 \u00b5L of elution buffer at 65 \u00b0C for 30 min. ChIP seq: To prepare the library eluted chromatin was reverse crosslinked and purified by phenol chloroform extraction. Then DNA was end repaired by END IT DNA end repair kit Epicentre ER81050 according to kit's protocol added A using Klenow fragment three prime >five prime exo NEB M0212S ligated with Illumina TruSeq adaptor Illumina FC 121 3001 and subsequently amplified by PCR Roche kk2601. The quality and quantity of all the libraries were checked using BioAnalyzer High Sensitivity DNA Kit Agilent. The libraries were sequenced on Illumina HiSeq 2500 with reads length of 2X 50 bp or 2X 100 bp. ATAC seq: Tuebingen adult tissues were ground in liquid nitrogen resuspended in 1 mL of lysis buffer 1X PBS 0.2% NP 40 5% BSA 1 mM DTT protease inhibitors followed by incubation at 4 \u00b0C for 10 min on an overhead shaker. post that lysate was filtered through 40 \uf06dm cell strainer and nuclei were collected at 1000X g for 5 min. ATAC seq: Tagmentation was performed immediately according to ATAC seq protocol reported previouslyBuenrostro et al. 2013 Hi C: For brain tissue two adult Tuebingen brains were slightly ground into small granules in liquid nitrogen and resuspended in 1 mL of cold hypotonic buffer 20 mM Tris HCl pH 8.0 10 mM NaCl 20 mM EDTA. Granular brains were then dounce homogenized with loose pestle for 20 times. The top of the homogenate was carefully transferred into a new tube and fixed with 2% formaldehyde at room temperature for 10 min. 0.2 M of glycine was added to stop fixation. For muscle tissue 60 mg of Tuebingen muscle was first chopped into small pieces and digested by 0.25% trypsin at room temperature for 30 min. post neutralization with FBS muscle cells were resuspended in cold 1X PBS and fixed with 2% of formaldehyde at room temperature for 10 min. 0.2 M glycine was then added to stop fixation. Hi C: Hi C experiments on adult zebrafish brain and muscle tissues were performed according to previously published protocolRao et al. 2014. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 100 bp high throughput sequencing using HiSeq 2500 or HiSeq 4000Illumina. WGBS: T\u00fcbingen adult tissues were dissected and the genomic DNA was extracted using DNeasy Blood & Tissue Kit Qiagen 69504. Then 1 \u00b5g of genomic DNA of each adult tissue was subjected to bisulfite conversion using EZ DNA Methylation Gold Kits WGBS: The final libraries were prepared using the Accel NGS\u00ae Methyl Seq DNA Library Kit. scATAC seq: Single cell ATAC seq scATAC seq was performed in one female brain and one male brain respectively on the 10X Genomics platform. To isolate nuclei freshly dissected single brain was transferred to 1 mL NbActiv1 medium BrainBits NbActiv1 500 with a wide bore pipette tip to break the tissue into small pieces. Then the tissue was broken up completely using regular bore pipette tips followed by filtering through a 30 \u00b5m cell strainer. The isolated cells were spun down at 500 g for 5 min at 4 \u00b0C and then lysed in 100 \u00b5L chilled 0.1X Lysis Buffer 10 mM Tris HCl pH 7.5 10 mM NaCl 3 mM MgCl2 1% BSA 0.01% Tween 20 0.01% NP40 and 0.001% digitonin on ice for 5 min. Then 1 mL chilled Wash Buffer 10 mM Tris HCl pH 7.5 10 mM NaCl 3 mM MgCl2 1% BSA 0.1% Tween 20 was added to the lysed cells and cells were spun down at 500 g for 5 min at 4 \u00b0C. At last 300 \u00b5L chilled Diluted Nuclei Buffer 10x Genomics PN 2000153/2000207 was added to resuspend the nuclei. The nuclei were filtered again using a 30 \u00b5m cell strainer before cell counting scATAC seq: Around 12 000 nuclei were used for one Tn5 tagmentation reaction and the scATAC seq library was prepared and sequenced exactly according to the company's user guide.", "GEO Accession:GSM4662085", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP213938", null, null, "YueLab-RNA-seq-Blood-rep1_1.fastq.gz YueLab-RNA-seq-Blood-rep1_2.fastq.gz", "fastq fastq", 10181340496.0, 33713048.0, "GSM4662085 r1", "0:151 1:151", "A:2735674306;C:2352790027;G:2376786768;T:2715986044;N:103351", 151, 151, null, null, 2735674306, 2352790027, 2376786768, 2715986044, 103351, "SRX8688332", "SRS6966993", "SRA919194", "GEO", "Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine", 2, 0.91563, 0.91373, 0.11339, 0.11315, 0.82235, 0.82266, 0.48854, 0.48669, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "sc", "single_cell_droplet", "10x", null, "United States", "2020-07-08", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [53009, "SRR9662030", "SRX6422906", "SRS5079696", "SRP213938", "PRJNA553572", "A map of cis regulatory elements and 3D genome structures in zebrafish", "GSE134055", "Other", "The zebrafish has been widely used for the study of human disease and development as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome however has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects we performed RNA seq ATAC seq ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall we have identified 235 596 cis regulatory elements which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish human and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore through the analysis of Hi C data in zebrafish brain and muscle we observed different levels of 3D genome organization including compartment topological associating domains TADs and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3 RNA Seq 11 of them were examined using ATAC seq WGBS and ChIP seq H3K9me3 and H3K9me2 and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that for the samples GSM4661977 GSM4662088 [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.", null, "pubmed:33239788;pubmed:35649578", null, "YueLab RNA Seq Spleen rep2", "GSM3934898", null, "source name:Tissue|strain:Tuebingen|tissue:Spleen", "YueLab RNA Seq Spleen rep2", "RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks were called using MACS2 with the following setting: ChIP seq q value <10e 2 p value<10e 5 Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5 HiC matrix was generated using HiC Pro Genome build: zv10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged", "Tissue", null, "For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol\u00ae according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer\u2019s protocol. Briefly polyA RNA was purified from 1000\u00a0ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.", "Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions", "strain:Tuebingen|tissue:Spleen", "GSM3934898", "GSM3934898: YueLab RNA Seq Spleen rep2; Danio rerio; RNA Seq", "GSM3934898", null, "1", "For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol\u00ae according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly polyA RNA was purified from 1000\u00a0ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.", "GEO Accession:GSM3934898", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer", null, "SRP213938", null, null, "YueLab-RNA-Seq-Spleen-rep2_1.fastq.gz YueLab-RNA-Seq-Spleen-rep2_2.fastq.gz", "fastq fastq", 8309777463.0, 41837414.0, "GSM3934898 r1", "0:98.87 1:99.75", "A:2235106866;C:1723612712;G:1748992271;T:2601473305;N:592309", 98, 99, null, null, 2235106866, 1723612712, 1748992271, 2601473305, 592309, "SRX6422906", "SRS5079696", "SRA919194", "GEO", "Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine", 2, 0.9718, 0.97965, 0.15676, 0.11996, 0.7347, 0.73831, 0.49813, 0.50156, 99, 100, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-07-09", "Pharyngula", "Embryo", "Spleen", "Hematopoietic System"], [53010, "SRR9662029", "SRX6422905", "SRS5079695", "SRP213938", "PRJNA553572", "A map of cis regulatory elements and 3D genome structures in zebrafish", "GSE134055", "Other", "The zebrafish has been widely used for the study of human disease and development as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome however has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects we performed RNA seq ATAC seq ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall we have identified 235 596 cis regulatory elements which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish human and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore through the analysis of Hi C data in zebrafish brain and muscle we observed different levels of 3D genome organization including compartment topological associating domains TADs and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3 RNA Seq 11 of them were examined using ATAC seq WGBS and ChIP seq H3K9me3 and H3K9me2 and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that for the samples GSM4661977 GSM4662088 [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.", null, "pubmed:33239788;pubmed:35649578", null, "YueLab RNA Seq Spleen rep1", "GSM3934897", null, "source name:Tissue|strain:Tuebingen|tissue:Spleen", "YueLab RNA Seq Spleen rep1", "RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks were called using MACS2 with the following setting: ChIP seq q value <10e 2 p value<10e 5 Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5 HiC matrix was generated using HiC Pro Genome build: zv10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged", "Tissue", null, "For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol\u00ae according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer\u2019s protocol. Briefly polyA RNA was purified from 1000\u00a0ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.", "Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions", "strain:Tuebingen|tissue:Spleen", "GSM3934897", "GSM3934897: YueLab RNA Seq Spleen rep1; Danio rerio; RNA Seq", "GSM3934897", null, "1", "For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol\u00ae according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly polyA RNA was purified from 1000\u00a0ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.", "GEO Accession:GSM3934897", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer", null, "SRP213938", null, null, "YueLab-RNA-Seq-Spleen-rep1_1.fastq.gz YueLab-RNA-Seq-Spleen-rep1_2.fastq.gz", "fastq fastq", 1940987484.0, 9748717.0, "GSM3934897 r1", "0:99.62 1:99.48", "A:522271746;C:424963046;G:430836475;T:562779653;N:136564", 99, 99, null, null, 522271746, 424963046, 430836475, 562779653, 136564, "SRX6422905", "SRS5079695", "SRA919194", "GEO", "Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine", 2, 0.97325, 0.97976, 0.13741, 0.12217, 0.72129, 0.73261, 0.50119, 0.4956, 100, 99, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-07-09", "Pharyngula", "Embryo", "Spleen", "Hematopoietic System"], [55536, "SRR10532692", "SRX7216663", "SRS5719129", "SRP233258", "PRJNA591815", "Ago2 dependent processing allows miR 451 to evade the global microRNA turnover elicited during erythropoiesis", "PRJNA591815", "Other", "MicroRNAs are sequentially processed by two RNAse III enzymes Drosha and Dicer. miR 451 is the only known miRNA whose processing bypasses Dicer and instead relies on the slicer activity of Argonaute 2 Ago2. MiR 451 is highly conserved in vertebrates and regulates erythrocyte maturation where it becomes the most abundant miRNA. However the basis for the non canonical biogenesis of miR 451 is unclear. In this study we tested the hypothesis that miR 144 represses Dicer in a negative feedback loop during erythropoiesis and enhances miR 451 biogenesis. Loss of miR 144 mediated Dicer repression in zebrafish embryos and human cells leads to increased canonical miRNA production and impaired miR 451 maturation.", null, null, null, null, "miR 451 mutant", null, "isolate:Lab reared|age:2 days|sex:not applicable|tissue:peripheral blood|genotype:miR 451 / |phenotype:wild type|treatment:n1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic profiling of peripheral blood from 2 dpf zebrafish embryos", "mRNA Mut miR 451", "mRNA Mut miR 451", "mRNA libraries were cloned from polyA+ RNA isolated from peripheral blood of 2 dpf WT and mutant zebrafish embryos according to Illumina TruSeq protocol. Libraries were cloned and sequenced at Boston University Microarray and Sequencing core.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233258", null, null, "mRNA-miR-451.fastq.gz", "fastq", 7904410367.0, 104613601.0, "mRNA miR 451.fastq.gz", "0:75.56 1:0", "A:1795110678;C:2004074141;G:2113982350;T:1989843693;N:1399505", 75, 0, null, null, 1795110678, 2004074141, 2113982350, 1989843693, 1399505, "SRX7216663", "SRS5719129", "SRA1002853", "University of East Anglia|Biological Sciences", "University of East Anglia", 1, 0.97314, null, 0.03847, null, 0.81744, null, 0.4673, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-11-26", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [55537, "SRR10532693", "SRX7216662", "SRS5719128", "SRP233258", "PRJNA591815", "Ago2 dependent processing allows miR 451 to evade the global microRNA turnover elicited during erythropoiesis", "PRJNA591815", "Other", "MicroRNAs are sequentially processed by two RNAse III enzymes Drosha and Dicer. miR 451 is the only known miRNA whose processing bypasses Dicer and instead relies on the slicer activity of Argonaute 2 Ago2. MiR 451 is highly conserved in vertebrates and regulates erythrocyte maturation where it becomes the most abundant miRNA. However the basis for the non canonical biogenesis of miR 451 is unclear. In this study we tested the hypothesis that miR 144 represses Dicer in a negative feedback loop during erythropoiesis and enhances miR 451 biogenesis. Loss of miR 144 mediated Dicer repression in zebrafish embryos and human cells leads to increased canonical miRNA production and impaired miR 451 maturation.", null, null, null, null, "miR 144 mutant", null, "isolate:Lab reared|age:2 days|sex:not applicable|tissue:peripheral blood|genotype:miR 144 / |phenotype:wild type|treatment:n1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic profiling of peripheral blood from 2 dpf zebrafish embryos", "mRNA Mut miR 144", "mRNA Mut miR 144", "mRNA libraries were cloned from polyA+ RNA isolated from peripheral blood of 2 dpf WT and mutant zebrafish embryos according to Illumina TruSeq protocol. Libraries were cloned and sequenced at Boston University Microarray and Sequencing core.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233258", null, null, "mRNA-miR-144.fastq.gz", "fastq", 21666521349.0, 286736059.0, "mRNA miR 144.fastq.gz", "0:75.56 1:0", "A:4937891523;C:5429635867;G:5884853915;T:5410789187;N:3350857", 75, 0, null, null, 4937891523, 5429635867, 5884853915, 5410789187, 3350857, "SRX7216662", "SRS5719128", "SRA1002853", "University of East Anglia|Biological Sciences", "University of East Anglia", 1, 0.97729, null, 0.02379, null, 0.84102, null, 0.45517, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-11-26", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [55538, "SRR10532694", "SRX7216661", "SRS5719127", "SRP233258", "PRJNA591815", "Ago2 dependent processing allows miR 451 to evade the global microRNA turnover elicited during erythropoiesis", "PRJNA591815", "Other", "MicroRNAs are sequentially processed by two RNAse III enzymes Drosha and Dicer. miR 451 is the only known miRNA whose processing bypasses Dicer and instead relies on the slicer activity of Argonaute 2 Ago2. MiR 451 is highly conserved in vertebrates and regulates erythrocyte maturation where it becomes the most abundant miRNA. However the basis for the non canonical biogenesis of miR 451 is unclear. In this study we tested the hypothesis that miR 144 represses Dicer in a negative feedback loop during erythropoiesis and enhances miR 451 biogenesis. Loss of miR 144 mediated Dicer repression in zebrafish embryos and human cells leads to increased canonical miRNA production and impaired miR 451 maturation.", null, null, null, null, "wild type", null, "isolate:Lab reared|age:2 days|sex:not applicable|tissue:peripheral blood|genotype:wild type|phenotype:wild type|treatment:n1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptomic profiling of peripheral blood from 2 dpf zebrafish embryos", "mRNA WT", "mRNA WT", "mRNA libraries were cloned from polyA+ RNA isolated from peripheral blood of 2 dpf WT and mutant zebrafish embryos according to Illumina TruSeq protocol. Libraries were cloned and sequenced at Boston University Microarray and Sequencing core.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233258", null, null, "mRNA-WT.fastq.gz", "fastq", 5359234061.0, 70925969.0, "mRNA WT.fastq.gz", "0:75.56 1:0", "A:1229417939;C:1341096472;G:1448568683;T:1339375309;N:775658", 75, 0, null, null, 1229417939, 1341096472, 1448568683, 1339375309, 775658, "SRX7216661", "SRS5719127", "SRA1002853", "University of East Anglia|Biological Sciences", "University of East Anglia", 1, 0.97314, null, 0.02809, null, 0.83179, null, 0.40499, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-11-26", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [55539, "SRR10532695", "SRX7216660", "SRS5719128", "SRP233258", "PRJNA591815", "Ago2 dependent processing allows miR 451 to evade the global microRNA turnover elicited during erythropoiesis", "PRJNA591815", "Other", "MicroRNAs are sequentially processed by two RNAse III enzymes Drosha and Dicer. miR 451 is the only known miRNA whose processing bypasses Dicer and instead relies on the slicer activity of Argonaute 2 Ago2. MiR 451 is highly conserved in vertebrates and regulates erythrocyte maturation where it becomes the most abundant miRNA. However the basis for the non canonical biogenesis of miR 451 is unclear. In this study we tested the hypothesis that miR 144 represses Dicer in a negative feedback loop during erythropoiesis and enhances miR 451 biogenesis. Loss of miR 144 mediated Dicer repression in zebrafish embryos and human cells leads to increased canonical miRNA production and impaired miR 451 maturation.", null, null, null, null, "miR 144 mutant", null, "isolate:Lab reared|age:2 days|sex:not applicable|tissue:peripheral blood|genotype:miR 144 / |phenotype:wild type|treatment:n1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNA from peripheral blood from 2 dpf zebrafish embryos miR 451 mutant", "sRNA Mut miR 144", "sRNA Mut miR 144", "Small RNA libraries were prepared from total RNA 0.5 g isolated from peripheral blood of wild type WT and miR 144 / embryos at 48 hpf Small RNAs were size selected in 10% denaturing polyacrylamide gel in 1X TBE in range from 18 to 75 bp. RNA extraction from the gel was achieved by incubation in 0.3 M NaCl overnight at 4C with following precipitation with isopropanol. Pre adenylated 3 custom adaptor WT: /5PHOS/N*NCACAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC/3ddC/; miR 144 / :/5PHOS/N*NAGAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC/3ddC/ were ligated to small RNAs by T4 RNA ligase for 2 h at 22 C. post ligated products were size selected by gel from non ligated adaptor. Reverse transcription was performed by SuperScript III Reverse Transcription kit Thermo Fisher using custom RT Cloning Primer /5PHOS/NNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC SPC18 GGATCC SPC18 GTGACTGGAGTTCAGACGTGTGCTC. Then cDNA products were isolated by gel selection and then circularized by CircLigase ssDNA Ligase Epicentre. cDNA libraries were amplified in reactions containing forward and reverse Illumina index primers.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233258", null, null, "sRNA-miR-144.fastq.gz", "fastq", 284208421.0, 7813754.0, "sRNA miR 144.fastq.gz", "0:36.37", "A:63063755;C:66933795;G:92235682;T:61966771;N:8418", 36, null, null, null, 63063755, 66933795, 92235682, 61966771, 8418, "SRX7216660", "SRS5719128", "SRA1002853", "University of East Anglia|Biological Sciences", "University of East Anglia", 1, 0.02041, null, 0.00444, null, 0.98512, null, 0.44771, null, 28, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-11-26", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [55540, "SRR10532696", "SRX7216659", "SRS5719127", "SRP233258", "PRJNA591815", "Ago2 dependent processing allows miR 451 to evade the global microRNA turnover elicited during erythropoiesis", "PRJNA591815", "Other", "MicroRNAs are sequentially processed by two RNAse III enzymes Drosha and Dicer. miR 451 is the only known miRNA whose processing bypasses Dicer and instead relies on the slicer activity of Argonaute 2 Ago2. MiR 451 is highly conserved in vertebrates and regulates erythrocyte maturation where it becomes the most abundant miRNA. However the basis for the non canonical biogenesis of miR 451 is unclear. In this study we tested the hypothesis that miR 144 represses Dicer in a negative feedback loop during erythropoiesis and enhances miR 451 biogenesis. Loss of miR 144 mediated Dicer repression in zebrafish embryos and human cells leads to increased canonical miRNA production and impaired miR 451 maturation.", null, null, null, null, "wild type", null, "isolate:Lab reared|age:2 days|sex:not applicable|tissue:peripheral blood|genotype:wild type|phenotype:wild type|treatment:n1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNA from peripheral blood from 2 dpf zebrafish embryos wild type", "sRNA WT", "sRNA WT", "Small RNA libraries were prepared from total RNA 0.5 g isolated from peripheral blood of wild type WT and miR 144 / embryos at 48 hpf Small RNAs were size selected in 10% denaturing polyacrylamide gel in 1X TBE in range from 18 to 75 bp. RNA extraction from the gel was achieved by incubation in 0.3 M NaCl overnight at 4C with following precipitation with isopropanol. Pre adenylated 3 custom adaptor WT: /5PHOS/N*NCACAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC/3ddC/; miR 144 / :/5PHOS/N*NAGAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC/3ddC/ were ligated to small RNAs by T4 RNA ligase for 2 h at 22 C. post ligated products were size selected by gel from non ligated adaptor. Reverse transcription was performed by SuperScript III Reverse Transcription kit Thermo Fisher using custom RT Cloning Primer /5PHOS/NNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC SPC18 GGATCC SPC18 GTGACTGGAGTTCAGACGTGTGCTC. Then cDNA products were isolated by gel selection and then circularized by CircLigase ssDNA Ligase Epicentre. cDNA libraries were amplified in reactions containing forward and reverse Illumina index primers.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233258", null, null, "sRNA-WT.fastq.gz", "fastq", 294275059.0, 8550051.0, "sRNA WT.fastq.gz", "0:34.42", "A:65237071;C:85092331;G:80441993;T:63494506;N:9158", 34, null, null, null, 65237071, 85092331, 80441993, 63494506, 9158, "SRX7216659", "SRS5719127", "SRA1002853", "University of East Anglia|Biological Sciences", "University of East Anglia", 1, 0.00854, null, 0.00213, null, 0.99184, null, 0.55467, null, 31, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-11-26", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [58407, "SRR11309042", "SRX7913591", "SRS6320433", "SRP252869", "PRJNA612697", "RNA seq of hematopoietic stem and progenitor cells from 40 hpf ddx41 mutant and sibling zebrafish", "GSE146995", "Transcriptome Analysis", "The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development. Overall design: mRNA profiling of cd41 positive hematopoietic stem and progenitor cells isolated from 40 hpf ddx41 mutant and sibling zebrafish using Illumina NovaSeq. Three samples were sequenced for each genotype.", null, "pubmed:33651979", null, "cd41gfp WT3", "GSM4411870", null, "tissue:hematopoietic stem and progenitor cells|develpmental stage:40 hpf", "cd41gfp WT3", "basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file include gene counts for each sample", "hematopoietic stem and progenitor cells", null, "cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.", null, "develpmental stage:40 hpf", "GSM4411870", "GSM4411870: cd41gfp WT3; Danio rerio; RNA Seq", "GSM4411870", null, "1", "cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.", "GEO Accession:GSM4411870", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP252869", null, null, "cd41gfp_WT3_2.fq.gz cd41gfp_WT3_1.fq.gz", "fastq fastq", 11085766500.0, 36952555.0, "GSM4411870 r1", "0:150 1:150", "A:2992020230;C:2573519486;G:2581891304;T:2938153427;N:182053", 150, 150, null, null, 2992020230, 2573519486, 2581891304, 2938153427, 182053, "SRX7913591", "SRS6320433", "SRA1055135", "GEO", "Albert Einstein College of Medicine", 2, 0.77434, 0.77183, 0.20553, 0.20573, 0.77171, 0.77922, 0.5109, 0.495, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-03-15", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [58408, "SRR11309041", "SRX7913590", "SRS6320432", "SRP252869", "PRJNA612697", "RNA seq of hematopoietic stem and progenitor cells from 40 hpf ddx41 mutant and sibling zebrafish", "GSE146995", "Transcriptome Analysis", "The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development. Overall design: mRNA profiling of cd41 positive hematopoietic stem and progenitor cells isolated from 40 hpf ddx41 mutant and sibling zebrafish using Illumina NovaSeq. Three samples were sequenced for each genotype.", null, "pubmed:33651979", null, "cd41gfp WT2", "GSM4411869", null, "tissue:hematopoietic stem and progenitor cells|develpmental stage:40 hpf", "cd41gfp WT2", "basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file include gene counts for each sample", "hematopoietic stem and progenitor cells", null, "cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.", null, "develpmental stage:40 hpf", "GSM4411869", "GSM4411869: cd41gfp WT2; Danio rerio; RNA Seq", "GSM4411869", null, "1", "cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.", "GEO Accession:GSM4411869", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP252869", null, null, "cd41gfp_WT2_1.fq.gz cd41gfp_WT2_2.fq.gz", "fastq fastq", 11221423200.0, 37404744.0, "GSM4411869 r1", "0:150 1:150", "A:2921284710;C:2714470786;G:2708278380;T:2877145192;N:244132", 150, 150, null, null, 2921284710, 2714470786, 2708278380, 2877145192, 244132, "SRX7913590", "SRS6320432", "SRA1055135", "GEO", "Albert Einstein College of Medicine", 2, 0.75116, 0.75065, 0.18086, 0.18146, 0.79586, 0.80016, 0.52492, 0.52828, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-03-15", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [58409, "SRR11309040", "SRX7913589", "SRS6320431", "SRP252869", "PRJNA612697", "RNA seq of hematopoietic stem and progenitor cells from 40 hpf ddx41 mutant and sibling zebrafish", "GSE146995", "Transcriptome Analysis", "The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development. Overall design: mRNA profiling of cd41 positive hematopoietic stem and progenitor cells isolated from 40 hpf ddx41 mutant and sibling zebrafish using Illumina NovaSeq. Three samples were sequenced for each genotype.", null, "pubmed:33651979", null, "cd41gfp WT1", "GSM4411868", null, "tissue:hematopoietic stem and progenitor cells|develpmental stage:40 hpf", "cd41gfp WT1", "basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file include gene counts for each sample", "hematopoietic stem and progenitor cells", null, "cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.", null, "develpmental stage:40 hpf", "GSM4411868", "GSM4411868: cd41gfp WT1; Danio rerio; RNA Seq", "GSM4411868", null, "1", "cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.", "GEO Accession:GSM4411868", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP252869", null, null, "cd41gfp_WT1_1.fq.gz cd41gfp_WT1_2.fq.gz", "fastq fastq", 11115852900.0, 37052843.0, "GSM4411868 r1", "0:150 1:150", "A:3004371197;C:2577587578;G:2575472481;T:2958199318;N:222326", 150, 150, null, null, 3004371197, 2577587578, 2575472481, 2958199318, 222326, "SRX7913589", "SRS6320431", "SRA1055135", "GEO", "Albert Einstein College of Medicine", 2, 0.76528, 0.76415, 0.19581, 0.19637, 0.77039, 0.77579, 0.65251, 0.64941, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-03-15", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [58410, "SRR11309039", "SRX7913588", "SRS6320430", "SRP252869", "PRJNA612697", "RNA seq of hematopoietic stem and progenitor cells from 40 hpf ddx41 mutant and sibling zebrafish", "GSE146995", "Transcriptome Analysis", "The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development. Overall design: mRNA profiling of cd41 positive hematopoietic stem and progenitor cells isolated from 40 hpf ddx41 mutant and sibling zebrafish using Illumina NovaSeq. Three samples were sequenced for each genotype.", null, "pubmed:33651979", null, "cd41gfp mut3", "GSM4411867", null, "tissue:hematopoietic stem and progenitor cells|develpmental stage:40 hpf mutant", "cd41gfp mut3", "basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file include gene counts for each sample", "hematopoietic stem and progenitor cells", null, "cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.", null, "develpmental stage:40 hpf mutant", "GSM4411867", "GSM4411867: cd41gfp mut3; Danio rerio; RNA Seq", "GSM4411867", null, "1", "cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.", "GEO Accession:GSM4411867", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP252869", null, null, "cd41gfp_mut3_2.fq.gz cd41gfp_mut3_1.fq.gz", "fastq fastq", 11157315900.0, 37191053.0, "GSM4411867 r1", "0:150 1:150", "A:2980738665;C:2622591667;G:2625477229;T:2928292016;N:216323", 150, 150, null, null, 2980738665, 2622591667, 2625477229, 2928292016, 216323, "SRX7913588", "SRS6320430", "SRA1055135", "GEO", "Albert Einstein College of Medicine", 2, 0.77032, 0.76857, 0.22483, 0.22518, 0.78685, 0.79226, 0.64484, 0.52439, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-03-15", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [58411, "SRR11309038", "SRX7913587", "SRS6320429", "SRP252869", "PRJNA612697", "RNA seq of hematopoietic stem and progenitor cells from 40 hpf ddx41 mutant and sibling zebrafish", "GSE146995", "Transcriptome Analysis", "The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development. Overall design: mRNA profiling of cd41 positive hematopoietic stem and progenitor cells isolated from 40 hpf ddx41 mutant and sibling zebrafish using Illumina NovaSeq. Three samples were sequenced for each genotype.", null, "pubmed:33651979", null, "cd41gfp mut2", "GSM4411866", null, "tissue:hematopoietic stem and progenitor cells|develpmental stage:40 hpf mutant", "cd41gfp mut2", "basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file include gene counts for each sample", "hematopoietic stem and progenitor cells", null, "cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.", null, "develpmental stage:40 hpf mutant", "GSM4411866", "GSM4411866: cd41gfp mut2; Danio rerio; RNA Seq", "GSM4411866", null, "1", "cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.", "GEO Accession:GSM4411866", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP252869", null, null, "cd41gfp_mut2_1.fq.gz cd41gfp_mut2_2.fq.gz", "fastq fastq", 10547871900.0, 35159573.0, "GSM4411866 r1", "0:150 1:150", "A:2823130170;C:2469329724;G:2474038085;T:2781202013;N:171908", 150, 150, null, null, 2823130170, 2469329724, 2474038085, 2781202013, 171908, "SRX7913587", "SRS6320429", "SRA1055135", "GEO", "Albert Einstein College of Medicine", 2, 0.77081, 0.76762, 0.19951, 0.20063, 0.78518, 0.7905, 0.62792, 0.62645, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-03-15", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [58412, "SRR11309037", "SRX7913586", "SRS6320428", "SRP252869", "PRJNA612697", "RNA seq of hematopoietic stem and progenitor cells from 40 hpf ddx41 mutant and sibling zebrafish", "GSE146995", "Transcriptome Analysis", "The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development. Overall design: mRNA profiling of cd41 positive hematopoietic stem and progenitor cells isolated from 40 hpf ddx41 mutant and sibling zebrafish using Illumina NovaSeq. Three samples were sequenced for each genotype.", null, "pubmed:33651979", null, "cd41gfp mut1", "GSM4411865", null, "tissue:hematopoietic stem and progenitor cells|develpmental stage:40 hpf mutant", "cd41gfp mut1", "basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. To calculate FPKM Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file include gene counts for each sample", "hematopoietic stem and progenitor cells", null, "cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.", null, "develpmental stage:40 hpf mutant", "GSM4411865", "GSM4411865: cd41gfp mut1; Danio rerio; RNA Seq", "GSM4411865", null, "1", "cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.", "GEO Accession:GSM4411865", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP252869", null, null, "cd41gfp_mut1_2.fq.gz cd41gfp_mut1_1.fq.gz", "fastq fastq", 11189402700.0, 37298009.0, "GSM4411865 r1", "0:150 1:150", "A:2871209944;C:2750231891;G:2743649245;T:2824098453;N:213167", 150, 150, null, null, 2871209944, 2750231891, 2743649245, 2824098453, 213167, "SRX7913586", "SRS6320428", "SRA1055135", "GEO", "Albert Einstein College of Medicine", 2, 0.74106, 0.73935, 0.17858, 0.18025, 0.80574, 0.81231, 0.60677, 0.65263, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-03-15", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [63788, "SRR14055354", "SRX10431257", "SRS8565312", "SRP311888", "PRJNA716463", "Mutation of smarca5 in zebrafish leads to venous thrombosis like phenotype", "PRJNA716463", "Other", "Our study using zebrafish smarca5 mutants both characterizes a novel role for smarca5 in blood clot formation and also provides a new venous thrombosis animal model to support drug screening and pre clinical therapeutic assessments of therapies to treat thrombosis.", null, null, null, "Model organism or animal sample from Danio rerio", "RNA RBC mutant rep3", null, "strain:gata1:dsRed transgenic line|dev stage:2 dpf|sex:not collected|tissue:Blood|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA RBC mutant rep3", "RNA RBC mutant rep3", "RNA RBC mutant rep3", "PolyA RNA from 100 200ng total RNA in sorted RBCs from smarca5 siblings and mutants at 2 dpf were used to generate the cDNA libraries respectively", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP311888", null, null, "1049RBC-mu-3_FRAS190320004-1a_1.fq.gz 1049RBC-mu-3_FRAS190320004-1a_2.fq.gz", "fastq fastq", 13709534700.0, 45698449.0, "1049RBC mu 3 FRAS190320004 1a 1.fq.gz", "0:150 1:150", "A:3530756610;C:3372588726;G:3372560453;T:3433404064;N:224847", 150, 150, null, null, 3530756610, 3372588726, 3372560453, 3433404064, 224847, "SRX10431257", "SRS8565312", "SRA1209808", "Tsinghua university|School of Life Sciences", "Tsinghua university", 2, 0.92707, 0.92658, 0.05411, 0.05405, 0.75607, 0.75568, 0.45262, 0.45118, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-03-24", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [63789, "SRR14055355", "SRX10431256", "SRS8565311", "SRP311888", "PRJNA716463", "Mutation of smarca5 in zebrafish leads to venous thrombosis like phenotype", "PRJNA716463", "Other", "Our study using zebrafish smarca5 mutants both characterizes a novel role for smarca5 in blood clot formation and also provides a new venous thrombosis animal model to support drug screening and pre clinical therapeutic assessments of therapies to treat thrombosis.", null, null, null, "Model organism or animal sample from Danio rerio", "RNA RBC mutant rep2", null, "strain:gata1:dsRed transgenic line|dev stage:2 dpf|sex:not collected|tissue:Blood|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA RBC mutant rep2", "RNA RBC mutant rep2", "RNA RBC mutant rep2", "PolyA RNA from 100 200ng total RNA in sorted RBCs from smarca5 siblings and mutants at 2 dpf were used to generate the cDNA libraries respectively", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP311888", null, null, "1049RBC-mu-2_FRAS190320003-1a_1.fq.gz 1049RBC-mu-2_FRAS190320003-1a_2.fq.gz", "fastq fastq", 11921348400.0, 39737828.0, "1049RBC mu 2 FRAS190320003 1a 1.fq.gz", "0:150 1:150", "A:3056981846;C:2949479942;G:2955534362;T:2959157195;N:195055", 150, 150, null, null, 3056981846, 2949479942, 2955534362, 2959157195, 195055, "SRX10431256", "SRS8565311", "SRA1209808", "Tsinghua university|School of Life Sciences", "Tsinghua university", 2, 0.92527, 0.92379, 0.04988, 0.05004, 0.76629, 0.76723, 0.45068, 0.44998, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-03-24", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [63790, "SRR14055358", "SRX10431253", "SRS8565308", "SRP311888", "PRJNA716463", "Mutation of smarca5 in zebrafish leads to venous thrombosis like phenotype", "PRJNA716463", "Other", "Our study using zebrafish smarca5 mutants both characterizes a novel role for smarca5 in blood clot formation and also provides a new venous thrombosis animal model to support drug screening and pre clinical therapeutic assessments of therapies to treat thrombosis.", null, null, null, "Model organism or animal sample from Danio rerio", "RNA RBC mutant rep1", null, "strain:gata1:dsRed transgenic line|dev stage:2 dpf|sex:not collected|tissue:Blood|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA RBC mutant rep1", "RNA RBC mutant rep1", "RNA RBC mutant rep1", "PolyA RNA from 100 200ng total RNA in sorted RBCs from smarca5 siblings and mutants at 2 dpf were used to generate the cDNA libraries respectively", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP311888", null, null, "1049RBC-mu-1_FRAS190320002-1a_1.fq.gz 1049RBC-mu-1_FRAS190320002-1a_2.fq.gz", "fastq fastq", 12136778100.0, 40455927.0, "1049RBC mu 1 FRAS190320002 1a 1.fq.gz", "0:150 1:150", "A:3129750481;C:2985406228;G:2964648069;T:3056774126;N:199196", 150, 150, null, null, 3129750481, 2985406228, 2964648069, 3056774126, 199196, "SRX10431253", "SRS8565308", "SRA1209808", "Tsinghua university|School of Life Sciences", "Tsinghua university", 2, 0.83132, 0.8312, 0.04768, 0.04763, 0.77455, 0.77508, 0.47219, 0.46709, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-03-24", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [63791, "SRR14055359", "SRX10431252", "SRS8565307", "SRP311888", "PRJNA716463", "Mutation of smarca5 in zebrafish leads to venous thrombosis like phenotype", "PRJNA716463", "Other", "Our study using zebrafish smarca5 mutants both characterizes a novel role for smarca5 in blood clot formation and also provides a new venous thrombosis animal model to support drug screening and pre clinical therapeutic assessments of therapies to treat thrombosis.", null, null, null, "Model organism or animal sample from Danio rerio", "RNA RBC sibling rep3", null, "strain:gata1:dsRed transgenic line|dev stage:2 dpf|sex:not collected|tissue:Blood|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA RBC sibling rep3", "RNA RBC sibling rep3", "RNA RBC sibling rep3", "PolyA RNA from 100 200ng total RNA in sorted RBCs from smarca5 siblings and mutants at 2 dpf were used to generate the cDNA libraries respectively", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP311888", null, null, "1049RBC-sib-3_FRAS190320001-1a_1.fq.gz 1049RBC-sib-3_FRAS190320001-1a_2.fq.gz", "fastq fastq", 13833315900.0, 46111053.0, "1049RBC sib 3 FRAS190320001 1a 1.fq.gz", "0:150 1:150", "A:3515133007;C:3462086735;G:3467124241;T:3388720799;N:251118", 150, 150, null, null, 3515133007, 3462086735, 3467124241, 3388720799, 251118, "SRX10431252", "SRS8565307", "SRA1209808", "Tsinghua university|School of Life Sciences", "Tsinghua university", 2, 0.93805, 0.93649, 0.04283, 0.04244, 0.80752, 0.80817, 0.44958, 0.44864, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-03-24", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [63792, "SRR14055360", "SRX10431251", "SRS8565306", "SRP311888", "PRJNA716463", "Mutation of smarca5 in zebrafish leads to venous thrombosis like phenotype", "PRJNA716463", "Other", "Our study using zebrafish smarca5 mutants both characterizes a novel role for smarca5 in blood clot formation and also provides a new venous thrombosis animal model to support drug screening and pre clinical therapeutic assessments of therapies to treat thrombosis.", null, null, null, "Model organism or animal sample from Danio rerio", "RNA RBC sibling rep2", null, "strain:gata1:dsRed transgenic line|dev stage:2 dpf|sex:not collected|tissue:Blood|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA RBC sibling rep2", "RNA RBC sibling rep2", "RNA RBC sibling rep2", "PolyA RNA from 100 200ng total RNA in sorted RBCs from smarca5 siblings and mutants at 2 dpf were used to generate the cDNA libraries respectively", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP311888", null, null, "1049RBC-sib-2_FRAS190320000-1a_1.fq.gz 1049RBC-sib-2_FRAS190320000-1a_2.fq.gz", "fastq fastq", 10846357200.0, 36154524.0, "1049RBC sib 2 FRAS190320000 1a 1.fq.gz", "0:150 1:150", "A:2755761785;C:2720527184;G:2723864022;T:2645998029;N:206180", 150, 150, null, null, 2755761785, 2720527184, 2723864022, 2645998029, 206180, "SRX10431251", "SRS8565306", "SRA1209808", "Tsinghua university|School of Life Sciences", "Tsinghua university", 2, 0.94927, 0.94734, 0.04134, 0.04034, 0.80505, 0.80586, 0.43562, 0.43266, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-03-24", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [63793, "SRR14055361", "SRX10431250", "SRS8565305", "SRP311888", "PRJNA716463", "Mutation of smarca5 in zebrafish leads to venous thrombosis like phenotype", "PRJNA716463", "Other", "Our study using zebrafish smarca5 mutants both characterizes a novel role for smarca5 in blood clot formation and also provides a new venous thrombosis animal model to support drug screening and pre clinical therapeutic assessments of therapies to treat thrombosis.", null, null, null, "Model organism or animal sample from Danio rerio", "RNA RBC sibling rep1", null, "strain:gata1:dsRed transgenic line|dev stage:2 dpf|sex:not collected|tissue:Blood|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA RBC sibling rep1", "RNA RBC sibling rep1", "RNA RBC sibling rep1", "PolyA RNA from 100 200ng total RNA in sorted RBCs from smarca5 siblings and mutants at 2 dpf were used to generate the cDNA libraries respectively", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP311888", null, null, "1049RBC-sib-1_FRAS190319999-1a_1.fq.gz 1049RBC-sib-1_FRAS190319999-1a_2.fq.gz", "fastq fastq", 10945070100.0, 36483567.0, "1049RBC sib 1 FRAS190319999 1a 1.fq.gz", "0:150 1:150", "A:2787518303;C:2738688307;G:2737440984;T:2681219061;N:203445", 150, 150, null, null, 2787518303, 2738688307, 2737440984, 2681219061, 203445, "SRX10431250", "SRS8565305", "SRA1209808", "Tsinghua university|School of Life Sciences", "Tsinghua university", 2, 0.94824, 0.94818, 0.04162, 0.04125, 0.80247, 0.80284, 0.44015, 0.43533, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-03-24", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65651, "SRR15483596", "SRX11783413", "SRS9786611", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "runx1:mCherry+ at 52 hpf #2 replicate", "GSM5525118", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:runx1+23:nls mCherry", "runx1:mCherry+ at 52 hpf #2 replicate", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:runx1+23:nls mCherry", "GSM5525118", "GSM5525118: runx1:mCherry+ at 52 hpf #2 replicate; Danio rerio; RNA Seq", "GSM5525118", null, "1", "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525118", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, "loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=R2 2 S1 L001 R1 001.fastq.gz read2PairFiles=R2 2 S1 L001 R2 001.fastq.gz read3PairFiles=R2 2 S1 L001 I1 001.fastq.gz", "R2-2_S1_L001_I1_001.fastq.gz R2-2_S1_L001_R1_001.fastq.gz R2-2_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 59162946612.0, 192087489.0, "GSM5525118 r1", "0:150 1:150 2:8", "A:6826510360;C:7720741166;G:7033747534;T:7231279942;N:844348", 150, 150, 8, null, 6826510360, 7720741166, 7033747534, 7231279942, 844348, "SRX11783413", "SRS9786611", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 1, 0.95266, null, 0.01784, null, 0.93022, null, 0.46235, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65652, "SRR15483597", "SRX11783413", "SRS9786611", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "runx1:mCherry+ at 52 hpf #2 replicate", "GSM5525118", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:runx1+23:nls mCherry", "runx1:mCherry+ at 52 hpf #2 replicate", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:runx1+23:nls mCherry", "GSM5525118", "GSM5525118: runx1:mCherry+ at 52 hpf #2 replicate; Danio rerio; RNA Seq", "GSM5525118", null, "1", "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525118", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, "loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=R2 2 S1 L002 R1 001.fastq.gz read2PairFiles=R2 2 S1 L002 R2 001.fastq.gz read3PairFiles=R2 2 S1 L002 I1 001.fastq.gz", "R2-2_S1_L002_I1_001.fastq.gz R2-2_S1_L002_R1_001.fastq.gz R2-2_S1_L002_R2_001.fastq.gz", "fastq fastq fastq", 67940768588.0, 220586911.0, "GSM5525118 r2", "0:150 1:150 2:8", "A:7901205395;C:8819719149;G:8118311347;T:8243562587;N:5238172", 150, 150, 8, null, 7901205395, 8819719149, 8118311347, 8243562587, 5238172, "SRX11783413", "SRS9786611", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 1, 0.94536, null, 0.018, null, 0.92839, null, 0.45489, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65653, "SRR15483594", "SRX11783412", "SRS9786609", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "runx1:mCherry+ at 52 hpf #1", "GSM5525117", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:runx1+23:nls mCherry", "runx1:mCherry+ at 52 hpf #1", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:runx1+23:nls mCherry", "GSM5525117", "GSM5525117: runx1:mCherry+ at 52 hpf #1; Danio rerio; RNA Seq", "GSM5525117", null, "1", "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525117", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, "loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=R2 1 S1 L001 R1 001.fastq.gz read2PairFiles=R2 1 S1 L001 R2 001.fastq.gz read3PairFiles=R2 1 S1 L001 I1 001.fastq.gz", "R2-1_S1_L001_I1_001.fastq.gz R2-1_S1_L001_R1_001.fastq.gz R2-1_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 64542996056.0, 209555182.0, "GSM5525117 r1", "0:150 1:150 2:8", "A:7500200023;C:8401456631;G:7492567345;T:8038123819;N:929482", 150, 150, 8, null, 7500200023, 8401456631, 7492567345, 8038123819, 929482, "SRX11783412", "SRS9786609", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 1, 0.94027, null, 0.01204, null, 0.94107, null, 0.46801, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65654, "SRR15483595", "SRX11783412", "SRS9786609", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "runx1:mCherry+ at 52 hpf #1", "GSM5525117", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:runx1+23:nls mCherry", "runx1:mCherry+ at 52 hpf #1", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:runx1+23:nls mCherry", "GSM5525117", "GSM5525117: runx1:mCherry+ at 52 hpf #1; Danio rerio; RNA Seq", "GSM5525117", null, "1", "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525117", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, "loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=R2 1 S1 L002 R1 001.fastq.gz read2PairFiles=R2 1 S1 L002 R2 001.fastq.gz read3PairFiles=R2 1 S1 L002 I1 001.fastq.gz", "R2-1_S1_L002_I1_001.fastq.gz R2-1_S1_L002_R1_001.fastq.gz R2-1_S1_L002_R2_001.fastq.gz", "fastq fastq fastq", 61129147772.0, 198471259.0, "GSM5525117 r2", "0:150 1:150 2:8", "A:7164346674;C:7911114850;G:7135136885;T:7555336618;N:4753823", 150, 150, 8, null, 7164346674, 7911114850, 7135136885, 7555336618, 4753823, "SRX11783412", "SRS9786609", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 1, 0.93152, null, 0.01164, null, 0.94152, null, 0.46255, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65655, "SRR15483588", "SRX11783411", "SRS9786608", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate", "GSM5525116", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "GSM5525116", "GSM5525116: draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate; Danio rerio; RNA Seq", "GSM5525116", null, "1", "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525116", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, "loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=DG2 2 S1 L001 R1 001.fastq.gz read2PairFiles=DG2 2 S1 L001 R2 001.fastq.gz read3PairFiles=DG2 2 S1 L001 I1 001.fastq.gz", "DG2-2_S1_L001_I1_001.fastq.gz DG2-2_S1_L001_R1_001.fastq.gz DG2-2_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 58062154920.0, 188513490.0, "GSM5525116 r1", "0:150 1:150 2:8", "A:6786904201;C:7461082970;G:6741279762;T:7286929534;N:827033", 150, 150, 8, null, 6786904201, 7461082970, 6741279762, 7286929534, 827033, "SRX11783411", "SRS9786608", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 1, 0.9442, null, 0.02532, null, 0.92577, null, 0.45185, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65656, "SRR15483589", "SRX11783411", "SRS9786608", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate", "GSM5525116", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "GSM5525116", "GSM5525116: draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate; Danio rerio; RNA Seq", "GSM5525116", null, "1", "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525116", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, "loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=DG2 2 S1 L002 R1 001.fastq.gz read2PairFiles=DG2 2 S1 L002 R2 001.fastq.gz read3PairFiles=DG2 2 S1 L002 I1 001.fastq.gz", "DG2-2_S1_L002_I1_001.fastq.gz DG2-2_S1_L002_R1_001.fastq.gz DG2-2_S1_L002_R2_001.fastq.gz", "fastq fastq fastq", 71629010068.0, 232561721.0, "GSM5525116 r2", "0:150 1:150 2:8", "A:8422157482;C:9164931651;G:8346143692;T:8946552575;N:4472750", 150, 150, 8, null, 8422157482, 9164931651, 8346143692, 8946552575, 4472750, "SRX11783411", "SRS9786608", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 1, 0.93666, null, 0.02678, null, 0.92232, null, 0.44942, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65657, "SRR15483590", "SRX11783411", "SRS9786608", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate", "GSM5525116", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "GSM5525116", "GSM5525116: draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate; Danio rerio; RNA Seq", "GSM5525116", null, "1", "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525116", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, null, "DG2-2_S1_L003_R1_001.fastq.gz DG2-2_S1_L003_R2_001.fastq.gz", "fastq fastq", 32047702200.0, 106825674.0, "GSM5525116 r3", "0:150 1:150", "A:7309683350;C:6236246000;G:6254785333;T:12244316725;N:2670792", 150, 150, null, null, 7309683350, 6236246000, 6254785333, 12244316725, 2670792, "SRX11783411", "SRS9786608", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 2, 0.01831, 0.94417, 0.00206, 0.02463, 0.99691, 0.92423, 0.53203, 0.45728, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65658, "SRR15483591", "SRX11783411", "SRS9786608", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate", "GSM5525116", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "GSM5525116", "GSM5525116: draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate; Danio rerio; RNA Seq", "GSM5525116", null, "1", "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525116", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, null, "DG2-2_S1_L004_R1_001.fastq.gz DG2-2_S1_L004_R2_001.fastq.gz", "fastq fastq", 37463959500.0, 124879865.0, "GSM5525116 r4", "0:150 1:150", "A:8552446843;C:7287672885;G:7301637904;T:14319175980;N:3025888", 150, 150, null, null, 8552446843, 7287672885, 7301637904, 14319175980, 3025888, "SRX11783411", "SRS9786608", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 2, 0.0179, 0.94533, 0.00191, 0.0243, 0.99691, 0.92261, 0.49722, 0.45421, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65659, "SRR15483592", "SRX11783411", "SRS9786608", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate", "GSM5525116", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "GSM5525116", "GSM5525116: draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate; Danio rerio; RNA Seq", "GSM5525116", null, "1", "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525116", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, null, "DG2-2_S1_L005_R1_001.fastq.gz DG2-2_S1_L005_R2_001.fastq.gz", "fastq fastq", 30981057900.0, 103270193.0, "GSM5525116 r5", "0:150 1:150", "A:7076201480;C:6026934261;G:6065200560;T:11810111130;N:2610469", 150, 150, null, null, 7076201480, 6026934261, 6065200560, 11810111130, 2610469, "SRX11783411", "SRS9786608", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 2, 0.01658, 0.93855, 0.00198, 0.02394, 0.99734, 0.92476, 0.53823, 0.45548, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65660, "SRR15483593", "SRX11783411", "SRS9786608", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate", "GSM5525116", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "GSM5525116", "GSM5525116: draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate; Danio rerio; RNA Seq", "GSM5525116", null, "1", "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525116", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, null, "DG2-2_S1_L006_R1_001.fastq.gz DG2-2_S1_L006_R2_001.fastq.gz", "fastq fastq", 33497811000.0, 111659370.0, "GSM5525116 r6", "0:150 1:150", "A:7673047524;C:6494998239;G:6520425795;T:12806463581;N:2875861", 150, 150, null, null, 7673047524, 6494998239, 6520425795, 12806463581, 2875861, "SRX11783411", "SRS9786608", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 2, 0.01712, 0.94074, 0.00206, 0.02516, 0.99701, 0.92318, 0.56268, 0.45333, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65661, "SRR15483582", "SRX11783410", "SRS9786606", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "draculin:mCherry+;gata1:GFP at 52 hpf #1", "GSM5525115", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "draculin:mCherry+;gata1:GFP at 52 hpf #1", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "GSM5525115", "GSM5525115: draculin:mCherry+;gata1:GFP at 52 hpf #1; Danio rerio; RNA Seq", "GSM5525115", null, "1", "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525115", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, "loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=DG2 1 S1 L001 R1 001.fastq.gz read2PairFiles=DG2 1 S1 L001 R2 001.fastq.gz read3PairFiles=DG2 1 S1 L001 I1 001.fastq.gz", "DG2-1_S1_L001_I1_001.fastq.gz DG2-1_S1_L001_R1_001.fastq.gz DG2-1_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 53816019796.0, 174727337.0, "GSM5525115 r1", "0:150 1:150 2:8", "A:6268319263;C:6935405810;G:6236287882;T:6768309909;N:777686", 150, 150, 8, null, 6268319263, 6935405810, 6236287882, 6768309909, 777686, "SRX11783410", "SRS9786606", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 1, 0.94373, null, 0.02418, null, 0.93206, null, 0.4538, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65662, "SRR15483583", "SRX11783410", "SRS9786606", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "draculin:mCherry+;gata1:GFP at 52 hpf #1", "GSM5525115", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "draculin:mCherry+;gata1:GFP at 52 hpf #1", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "GSM5525115", "GSM5525115: draculin:mCherry+;gata1:GFP at 52 hpf #1; Danio rerio; RNA Seq", "GSM5525115", null, "1", "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525115", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, "loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=DG2 1 S1 L002 R1 001.fastq.gz read2PairFiles=DG2 1 S1 L002 R2 001.fastq.gz read3PairFiles=DG2 1 S1 L002 I1 001.fastq.gz", "DG2-1_S1_L002_I1_001.fastq.gz DG2-1_S1_L002_R1_001.fastq.gz DG2-1_S1_L002_R2_001.fastq.gz", "fastq fastq fastq", 56656687472.0, 183950284.0, "GSM5525115 r2", "0:150 1:150 2:8", "A:6636746214;C:7271043747;G:6588518102;T:7092648593;N:3585944", 150, 150, 8, null, 6636746214, 7271043747, 6588518102, 7092648593, 3585944, "SRX11783410", "SRS9786606", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 1, 0.9348, null, 0.02385, null, 0.93156, null, 0.45273, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65663, "SRR15483584", "SRX11783410", "SRS9786606", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "draculin:mCherry+;gata1:GFP at 52 hpf #1", "GSM5525115", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "draculin:mCherry+;gata1:GFP at 52 hpf #1", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "GSM5525115", "GSM5525115: draculin:mCherry+;gata1:GFP at 52 hpf #1; Danio rerio; RNA Seq", "GSM5525115", null, "1", "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525115", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, null, "DG2-1_S1_L003_R1_001.fastq.gz DG2-1_S1_L003_R2_001.fastq.gz", "fastq fastq", 33218500800.0, 110728336.0, "GSM5525115 r3", "0:150 1:150", "A:7550847416;C:6408594085;G:6405597564;T:12826295610;N:27166125", 150, 150, null, null, 7550847416, 6408594085, 6405597564, 12826295610, 27166125, "SRX11783410", "SRS9786606", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 2, 0.02176, 0.94163, 0.00286, 0.02347, 0.99703, 0.92991, 0.46265, 0.45574, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65664, "SRR15483585", "SRX11783410", "SRS9786606", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "draculin:mCherry+;gata1:GFP at 52 hpf #1", "GSM5525115", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "draculin:mCherry+;gata1:GFP at 52 hpf #1", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "GSM5525115", "GSM5525115: draculin:mCherry+;gata1:GFP at 52 hpf #1; Danio rerio; RNA Seq", "GSM5525115", null, "1", "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525115", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, null, "DG2-1_S1_L004_R1_001.fastq.gz DG2-1_S1_L004_R2_001.fastq.gz", "fastq fastq", 33634915800.0, 112116386.0, "GSM5525115 r4", "0:150 1:150", "A:7645827173;C:6494042604;G:6493405590;T:12974094595;N:27545838", 150, 150, null, null, 7645827173, 6494042604, 6493405590, 12974094595, 27545838, "SRX11783410", "SRS9786606", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 2, 0.02104, 0.9407, 0.00263, 0.02247, 0.99701, 0.93257, 0.49246, 0.4561, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65665, "SRR15483586", "SRX11783410", "SRS9786606", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "draculin:mCherry+;gata1:GFP at 52 hpf #1", "GSM5525115", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "draculin:mCherry+;gata1:GFP at 52 hpf #1", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "GSM5525115", "GSM5525115: draculin:mCherry+;gata1:GFP at 52 hpf #1; Danio rerio; RNA Seq", "GSM5525115", null, "1", "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525115", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, null, "DG2-1_S1_L005_R1_001.fastq.gz DG2-1_S1_L005_R2_001.fastq.gz", "fastq fastq", 34113860700.0, 113712869.0, "GSM5525115 r5", "0:150 1:150", "A:7749471214;C:6598363925;G:6596788535;T:13141319294;N:27917732", 150, 150, null, null, 7749471214, 6598363925, 6596788535, 13141319294, 27917732, "SRX11783410", "SRS9786606", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 2, 0.02131, 0.94056, 0.0023, 0.02334, 0.99719, 0.93164, 0.50985, 0.45474, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65666, "SRR15483587", "SRX11783410", "SRS9786606", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "draculin:mCherry+;gata1:GFP at 52 hpf #1", "GSM5525115", null, "tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "draculin:mCherry+;gata1:GFP at 52 hpf #1", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:52 hpf line:draculin:mCherry;gata1:GFP", "GSM5525115", "GSM5525115: draculin:mCherry+;gata1:GFP at 52 hpf #1; Danio rerio; RNA Seq", "GSM5525115", null, "1", "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525115", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, null, "DG2-1_S1_L006_R1_001.fastq.gz DG2-1_S1_L006_R2_001.fastq.gz", "fastq fastq", 34597356600.0, 115324522.0, "GSM5525115 r6", "0:150 1:150", "A:7866654210;C:6690644103;G:6695640643;T:13316020558;N:28397086", 150, 150, null, null, 7866654210, 6690644103, 6695640643, 13316020558, 28397086, "SRX11783410", "SRS9786606", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 2, 0.02131, 0.94082, 0.00235, 0.02244, 0.99665, 0.93089, 0.53827, 0.45518, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [65667, "SRR15483581", "SRX11783409", "SRS9786607", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "draculin:mCherry+;gata1:GFP at 30 hpf #2 replicate", "GSM5525114", null, "tissue:hematopoietic cells|developmental stage:30 hpf line:draculin:mCherry;gata1:GFP", "draculin:mCherry+;gata1:GFP at 30 hpf #2 replicate", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:30 hpf line:draculin:mCherry;gata1:GFP", "GSM5525114", "GSM5525114: draculin:mCherry+;gata1:GFP at 30 hpf #2 replicate; Danio rerio; RNA Seq", "GSM5525114", null, "1", "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525114", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, "loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=DG1 3 S1 L001 R1 001.fastq.gz read2PairFiles=DG1 3 S1 L001 R2 001.fastq.gz read3PairFiles=DG1 3 S1 L001 I1 001.fastq.gz", "DG1-3_S1_L001_I1_001.fastq.gz DG1-3_S1_L001_R1_001.fastq.gz DG1-3_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 53654080172.0, 174201559.0, "GSM5525114 r1", "0:150 1:150 2:8", "A:6842604916;C:6327854414;G:6203934909;T:6755061460;N:778151", 150, 150, 8, null, 6842604916, 6327854414, 6203934909, 6755061460, 778151, "SRX11783409", "SRS9786607", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 1, 0.92988, null, 0.06632, null, 0.84691, null, 0.45741, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [65668, "SRR15483580", "SRX11783408", "SRS9786605", "SRP332734", "PRJNA755310", "Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae", "GSE182213", "Transcriptome Analysis", "The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate.", null, "pubmed:34525360", null, "draculin:mCherry+;gata1:GFP at 30 hpf #1", "GSM5525113", null, "tissue:hematopoietic cells|developmental stage:30 hpf line:draculin:mCherry;gata1:GFP", "draculin:mCherry+;gata1:GFP at 30 hpf #1", "Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities", "hematopoietic cells", null, "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", null, "developmental stage:30 hpf line:draculin:mCherry;gata1:GFP", "GSM5525113", "GSM5525113: draculin:mCherry+;gata1:GFP at 30 hpf #1; Danio rerio; RNA Seq", "GSM5525113", null, "1", "draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions.", "GEO Accession:GSM5525113", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP332734", null, "loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=DG1 2 S1 L001 R1 001.fastq.gz read2PairFiles=DG1 2 S1 L001 R2 001.fastq.gz read3PairFiles=DG1 2 S1 L001 I1 001.fastq.gz", "DG1-2_S1_L001_I1_001.fastq.gz DG1-2_S1_L001_R1_001.fastq.gz DG1-2_S1_L001_R2_001.fastq.gz", "fastq fastq fastq", 65514487192.0, 212709374.0, "GSM5525113 r1", "0:150 1:150 2:8", "A:8050271487;C:8057897221;G:7684156435;T:8113136954;N:944003", 150, 150, 8, null, 8050271487, 8057897221, 7684156435, 8113136954, 944003, "SRX11783408", "SRS9786605", "SRA1278863", "GEO", "Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine", 1, 0.94401, null, 0.03521, null, 0.88339, null, 0.35428, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-16", "Pharyngula", "Embryo", "Blood", "Hematopoietic System"], [67018, "SRR16973884", "SRX13164748", "SRS11095951", "SRP346708", "PRJNA781453", "WGBS and RNA seq of Danio rerio in HSPC generation", "GSE189072", "Other", "In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.", null, "pubmed:35502759", null, "HSC mut rep3 RNA", "GSM5694258", null, "tissue:hematopoietic stem cells|developmental stage:HSC|genotype:dnmt1 mutant|region:AGM", "HSC mut rep3 RNA", "Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters \" t Y m 0.04 bt2 end to end\" and \" known splicesite infile p 30 k 10 dta t\" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant", "hematopoietic stem cells", null, "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", null, "developmental stage:HSC|genotype:dnmt1 mutant|region:AGM", "GSM5694258", "GSM5694258: HSC mut rep3 RNA; Danio rerio; RNA Seq", "GSM5694258", null, "1", "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", "GEO Accession:GSM5694258", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP346708", null, "loader:fastq load.py", "HSC_sib_3_1_RNA.fq.gz HSC_sib_3_2_RNA.fq.gz", "fastq fastq", 8212205400.0, 27374018.0, "GSM5694258 r1", "0:150 1:150", "A:2309633599;C:1667340979;G:1773247570;T:2461956533;N:26719", 150, 150, null, null, 2309633599, 1667340979, 1773247570, 2461956533, 26719, "SRX13164748", "SRS11095951", "SRA1331007", "GEO", "Institute of Hematology and Blood Diseases Hospital", 2, 0.9402, 0.93297, 0.16899, 0.16784, 0.73089, 0.73665, 0.49638, 0.49263, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "strtseq", null, "China", "2021-11-18", "Undetermined", "Embryo", "Blood", "Hematopoietic System"], [67019, "SRR16973883", "SRX13164747", "SRS11095950", "SRP346708", "PRJNA781453", "WGBS and RNA seq of Danio rerio in HSPC generation", "GSE189072", "Other", "In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.", null, "pubmed:35502759", null, "HSC mut rep2 RNA", "GSM5694257", null, "tissue:hematopoietic stem cells|developmental stage:HSC|genotype:dnmt1 mutant|region:AGM", "HSC mut rep2 RNA", "Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters \" t Y m 0.04 bt2 end to end\" and \" known splicesite infile p 30 k 10 dta t\" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant", "hematopoietic stem cells", null, "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", null, "developmental stage:HSC|genotype:dnmt1 mutant|region:AGM", "GSM5694257", "GSM5694257: HSC mut rep2 RNA; Danio rerio; RNA Seq", "GSM5694257", null, "1", "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", "GEO Accession:GSM5694257", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP346708", null, null, "HSC_sib_2_1_RNA.fq.gz HSC_sib_2_2_RNA.fq.gz", "fastq fastq", 3426398100.0, 11421327.0, "GSM5694257 r1", "0:150 1:150", "A:946653601;C:712946549;G:748099225;T:1018648813;N:49912", 150, 150, null, null, 946653601, 712946549, 748099225, 1018648813, 49912, "SRX13164747", "SRS11095950", "SRA1331007", "GEO", "Institute of Hematology and Blood Diseases Hospital", 2, 0.94198, 0.95128, 0.10797, 0.10975, 0.78366, 0.78892, 0.46218, 0.45981, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "strtseq", null, "China", "2021-11-18", "Undetermined", "Embryo", "Blood", "Hematopoietic System"], [67020, "SRR16973881", "SRX13164745", "SRS11095948", "SRP346708", "PRJNA781453", "WGBS and RNA seq of Danio rerio in HSPC generation", "GSE189072", "Other", "In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.", null, "pubmed:35502759", null, "HSC sib rep3 RNA", "GSM5694255", null, "tissue:hematopoietic stem cells|developmental stage:HSC|genotype:sibling|region:AGM", "HSC sib rep3 RNA", "Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters \" t Y m 0.04 bt2 end to end\" and \" known splicesite infile p 30 k 10 dta t\" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant", "hematopoietic stem cells", null, "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", null, "developmental stage:HSC|genotype:sibling|region:AGM", "GSM5694255", "GSM5694255: HSC sib rep3 RNA; Danio rerio; RNA Seq", "GSM5694255", null, "1", "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", "GEO Accession:GSM5694255", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP346708", null, "loader:fastq load.py", "HSC_mut_3_1_RNA.fq.gz HSC_mut_3_2_RNA.fq.gz", "fastq fastq", 9049492800.0, 30164976.0, "GSM5694255 r1", "0:150 1:150", "A:2539831836;C:1839829118;G:1955216925;T:2714585195;N:29726", 150, 150, null, null, 2539831836, 1839829118, 1955216925, 2714585195, 29726, "SRX13164745", "SRS11095948", "SRA1331007", "GEO", "Institute of Hematology and Blood Diseases Hospital", 2, 0.94274, 0.93556, 0.16188, 0.1602, 0.73046, 0.73308, 0.49974, 0.49435, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "strtseq", null, "China", "2021-11-18", "Undetermined", "Embryo", "Blood", "Hematopoietic System"], [67021, "SRR16973880", "SRX13164744", "SRS11095947", "SRP346708", "PRJNA781453", "WGBS and RNA seq of Danio rerio in HSPC generation", "GSE189072", "Other", "In this study we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First we generated a comprehensive DNA methylation landscape of EHT which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein we identified that DNA methylation as epigenetic regulator participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.", null, "pubmed:35502759", null, "HSC sib rep2 RNA", "GSM5694254", null, "tissue:hematopoietic stem cells|developmental stage:HSC|genotype:sibling|region:AGM", "HSC sib rep2 RNA", "Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters \" t Y m 0.04 bt2 end to end\" and \" known splicesite infile p 30 k 10 dta t\" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of HSC sibling and HSC mutant", "hematopoietic stem cells", null, "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", null, "developmental stage:HSC|genotype:sibling|region:AGM", "GSM5694254", "GSM5694254: HSC sib rep2 RNA; Danio rerio; RNA Seq", "GSM5694254", null, "1", "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", "GEO Accession:GSM5694254", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP346708", null, null, "HSC_mut_2_1_RNA.fq.gz HSC_mut_2_2_RNA.fq.gz", "fastq fastq", 3488203500.0, 11627345.0, "GSM5694254 r1", "0:150 1:150", "A:993927631;C:700449875;G:737230481;T:1056544435;N:51078", 150, 150, null, null, 993927631, 700449875, 737230481, 1056544435, 51078, "SRX13164744", "SRS11095947", "SRA1331007", "GEO", "Institute of Hematology and Blood Diseases Hospital", 2, 0.93176, 0.93765, 0.14294, 0.14478, 0.75302, 0.7582, 0.49038, 0.48496, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "strtseq", null, "China", "2021-11-18", "Undetermined", "Embryo", "Blood", "Hematopoietic System"], [76522, "SRR24999166", "SRX20755041", "SRS18043618", "SRP445421", "PRJNA986547", "Znf687 recruits Brd4 Smrt complex to regulate gfi1aa expression during neutrophil development", "GSE235609", "Transcriptome Analysis", "Neutrophils are key component of the innate immune system in vertebrates. Diverse transcription factors and cofactors act in a well coordinated manner to ensure proper neutrophil development. Dysregulation of the transcriptional program triggering neutrophil differentiation is associated with various human hematologic disorders such as neutropenia neutrophilia and leukemia. In the current study we show the zinc finger protein Znf687 is a lineage specific transcription factor whose deficiency leads to an impaired neutrophil development in zebrafish. Mechanistically Znf687 functions as a negative regulator of gfi1aa a pivotal modulator in terminal granulopoiesis to regulate neutrophil maturation. Moreover we found BRD4 an important epigenetic regulator interacts with ZNF687 in neutrophils. Deficiency of brd4 results in similar defective neutrophil development as observed in znf687 mutant zebrafish. Biochemical and genetic analyses further reveal that instead of serving as a canonical transcriptional coactivator Brd4 directly interacts and bridges Znf687 and Smrt nuclear corepressor on gfi1aa gene's promoter to exert transcription repression. Overall our work not only indicates Znf687 and Brd4 are reciprocally required in promoting granulopoiesis but also provides new insights into the role of the two crucial regulators in transcriptional repression. Overall design: We found that Znf687 served as a transcription repressor.we speculated that the aberrant upregulation of certain downstream target of Znf687 would be responsible for the defective neutrophil differentiation. Then RNA sequencing RNA seq analyses were conducted in the remaining mpx+ cells isolated from Tgmpx:eGFP and znf687a MO injected Tgmpx:eGFP larvae at 48 hpf.", null, "pubmed:38326409", null, "Tgmpx:eGFP 2", "GSM7506191", null, "source name:hematopoietic|tissue:hematopoietic|cell line:mpx+|cell type:neutrophil|genotype:WT|treatment:control|geo loc name:missing|collection date:missing", "Tgmpx:eGFP 2", "We filter the low quality reads More than 20% of the bases qualities are lower than 10 reads with adaptors and reads with unknown bases N bases more than 5% to get the clean reads. We use fastp to filter. We use HISATv2.0.4 to do the mapping step. We mapped clean reads to reference using Bowtie2v2.2.6 and then calculate gene expression level with RSEMv1.2.12. Then we calculate pearson correlation between all samples using cor perform hierarchical clustering between all samples using hclust perform PCA analysis with all samples using princomp and draw the diagrams with ggplot2 with fuctions of R. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "hematopoietic", "mpx+ cells isolated from Tgmpx:eGFP and znf687a MO injected Tgmpx:eGFP larvae at 48 hpf.", "RNA was extracted from sorted cells using RNeasy Micro Qiagen Manchester UK 1 \u03bcg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS\u00ae Universal V8 RNA seq Library Prep Kit vazyme Technology Co. Ltd. Nanjing China .The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Navoseq6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer\u2019s instructions.", "Wild type zebrafish without xxx were used as blank to determine the background values in GFP controls.", "tissue:hematopoietic|cell line:mpx+|cell type:neutrophil|genotype:WT|treatment:control", "GSM7506191", "GSM7506191: Tgmpx:eGFP 2; Danio rerio; RNA Seq", "GSM7506191 r1", "GSM7506191", "1", "RNA was extracted from sorted cells using RNeasy Micro Qiagen Manchester UK 1 \u03bcg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS\u00ae Universal V8 RNA seq Library Prep Kit vazyme Technology Co. Ltd. Nanjing China .The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Navoseq6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP445421", null, null, "R21136162-qtsw-z003-mpx-11-11_combined_R1.fastq.gz R21136162-qtsw-z003-mpx-11-11_combined_R2.fastq.gz", "fastq fastq", 6391196700.0, 21303989.0, "GSM7506191 r1", "0:150 1:150", "A:1663138882;C:1355987073;G:1750924104;T:1621100160;N:46481", 150, 150, null, null, 1663138882, 1355987073, 1750924104, 1621100160, 46481, "SRX20755041", "SRS18043618", "SRA1660768", "CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics", "CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics", 2, 0.94347, 0.94088, 0.10896, 0.10794, 0.69522, 0.69824, 0.48646, 0.48484, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "China", "2023-06-22", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [76525, "SRR24999169", "SRX20755038", "SRS18043615", "SRP445421", "PRJNA986547", "Znf687 recruits Brd4 Smrt complex to regulate gfi1aa expression during neutrophil development", "GSE235609", "Transcriptome Analysis", "Neutrophils are key component of the innate immune system in vertebrates. Diverse transcription factors and cofactors act in a well coordinated manner to ensure proper neutrophil development. Dysregulation of the transcriptional program triggering neutrophil differentiation is associated with various human hematologic disorders such as neutropenia neutrophilia and leukemia. In the current study we show the zinc finger protein Znf687 is a lineage specific transcription factor whose deficiency leads to an impaired neutrophil development in zebrafish. Mechanistically Znf687 functions as a negative regulator of gfi1aa a pivotal modulator in terminal granulopoiesis to regulate neutrophil maturation. Moreover we found BRD4 an important epigenetic regulator interacts with ZNF687 in neutrophils. Deficiency of brd4 results in similar defective neutrophil development as observed in znf687 mutant zebrafish. Biochemical and genetic analyses further reveal that instead of serving as a canonical transcriptional coactivator Brd4 directly interacts and bridges Znf687 and Smrt nuclear corepressor on gfi1aa gene's promoter to exert transcription repression. Overall our work not only indicates Znf687 and Brd4 are reciprocally required in promoting granulopoiesis but also provides new insights into the role of the two crucial regulators in transcriptional repression. Overall design: We found that Znf687 served as a transcription repressor.we speculated that the aberrant upregulation of certain downstream target of Znf687 would be responsible for the defective neutrophil differentiation. Then RNA sequencing RNA seq analyses were conducted in the remaining mpx+ cells isolated from Tgmpx:eGFP and znf687a MO injected Tgmpx:eGFP larvae at 48 hpf.", null, "pubmed:38326409", null, "Tgmpx:eGFP 1", "GSM7506190", null, "source name:hematopoietic|tissue:hematopoietic|cell line:mpx+|cell type:neutrophil|genotype:WT|treatment:control|geo loc name:missing|collection date:missing", "Tgmpx:eGFP 1", "We filter the low quality reads More than 20% of the bases qualities are lower than 10 reads with adaptors and reads with unknown bases N bases more than 5% to get the clean reads. We use fastp to filter. We use HISATv2.0.4 to do the mapping step. We mapped clean reads to reference using Bowtie2v2.2.6 and then calculate gene expression level with RSEMv1.2.12. Then we calculate pearson correlation between all samples using cor perform hierarchical clustering between all samples using hclust perform PCA analysis with all samples using princomp and draw the diagrams with ggplot2 with fuctions of R. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include RPKM values for each Sample", "hematopoietic", "mpx+ cells isolated from Tgmpx:eGFP and znf687a MO injected Tgmpx:eGFP larvae at 48 hpf.", "RNA was extracted from sorted cells using RNeasy Micro Qiagen Manchester UK 1 \u03bcg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS\u00ae Universal V8 RNA seq Library Prep Kit vazyme Technology Co. Ltd. Nanjing China .The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Navoseq6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer\u2019s instructions.", "Wild type zebrafish without xxx were used as blank to determine the background values in GFP controls.", "tissue:hematopoietic|cell line:mpx+|cell type:neutrophil|genotype:WT|treatment:control", "GSM7506190", "GSM7506190: Tgmpx:eGFP 1; Danio rerio; RNA Seq", "GSM7506190 r1", "GSM7506190", "1", "RNA was extracted from sorted cells using RNeasy Micro Qiagen Manchester UK 1 \u03bcg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS\u00ae Universal V8 RNA seq Library Prep Kit vazyme Technology Co. Ltd. Nanjing China .The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Navoseq6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP445421", null, null, "R21136162-qtsw-z003-mpx-11-10_combined_R2.fastq.gz R21136162-qtsw-z003-mpx-11-10_combined_R1.fastq.gz", "fastq fastq", 7364874300.0, 24549581.0, "GSM7506190 r1", "0:150 1:150", "A:1988715009;C:1657810285;G:1778472191;T:1939822538;N:54277", 150, 150, null, null, 1988715009, 1657810285, 1778472191, 1939822538, 54277, "SRX20755038", "SRS18043615", "SRA1660768", "CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics", "CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics", 2, 0.94842, 0.94741, 0.10807, 0.10703, 0.69451, 0.69552, 0.4957, 0.49509, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "China", "2023-06-22", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [76585, "SRR25181149", "SRX20928872", "SRS18204809", "SRP447851", "PRJNA991987", "RNA seq for gata1+ cells in add1 mutant zebrafish embryos and siblings at 22 hpf", "GSE236659", "Transcriptome Analysis", "Adducin 1 Add1 functions primarily as a membrane cytoskeletal protein whereas Add1 contains a bipartite nuclear localization signal implying its special nuclear function. However the nuclear functional roles of Add1 apart from maintaining cytoskeletal stability remain unknown. Here we created add1 deficient zebrafish using Tol2 transposon mediated gene trapping and evaluated how add1 deficiency affected early hematopoiesis development. When add1 is lacking in zebrafish both the primitive erythropoiesis and definitive hematopoiesis are compromised and the primitive erythroblast cells are unable to develop into healthy erythrocytes. More significantly the RNA sequencing results demonstrated that the p53 pathway is activated in the add1 depletion erythroblast cells causing the erythroblasts to undergo apoptosis at the 14 somites stage and 24 hpf. Additionally the anemic phenotype and apoptosis in add1 deficient embryos can be partially rescued by p53 insufficiency. Taken together our findings show that add1 is critical for zebrafish erythropoiesis partially through the p53 mediated apoptotic pathway which expands the regulatory role of Add1 for nuclear function. Overall design: To better understand the nuclear specific function of add1 we used RNA seq to analyze transcriptome changes in gata1 EGFP positive cells sorted from add1 deficient embryos and siblings at 22 hpf when the differences in the number of erythrocytes were not yet evident in add1 mutant embryos. Comparative gene expression profiling analysis of RNA seq data for erythroblast of add1 mutant and siblings.", null, "pubmed:37636049", null, "WT", "GSM7567236", null, "tissue:erythroblast|cell type:erythroblast|genotype:wildtype|geo loc name:missing|collection date:missing", "WT", "For gene expression analysis the matched reads were calculated and then normalized to RPKM using RESM software The significance of the differential expression of genes was defined by the bioinformatics service of BGI according to the combination of the absolute value of log2 Ratio \u22651 and FDR \u2264 0.001. Library construction and sequencing were performed on a BGISEQ 500. Assembly: GRCz10.81 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file include RPKM values for each Sample", "erythroblast", null, "Total RNA was isolated using SMART Seq\u00ae HT Kit. Library construction and sequencing were performed on a BGISEQ 500 by CapitalBio Technology www.capitalbiotech.com Beijin China. Clean tags were mapped to the reference genome and genes available at the Zebrafish Genome.", null, "cell type:erythroblast|genotype:wildtype", "GSM7567236", "GSM7567236: WT; Danio rerio; RNA Seq", "GSM7567236 r1", "GSM7567236", "1", "Total RNA was isolated using SMART Seq\u00ae HT Kit. Library construction and sequencing were performed on a BGISEQ 500 by CapitalBio Technology www.capitalbiotech.com Beijin China. Clean tags were mapped to the reference genome and genes available at the Zebrafish Genome.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP447851", null, null, "WT_1.fq.gz WT_2.fq.gz", "fastq fastq", 6503251500.0, 21677505.0, "GSM7567236 r1", "0:150 1:150", "A:1785076844;C:1448752781;G:1570097457;T:1699269694;N:54724", 150, 150, null, null, 1785076844, 1448752781, 1570097457, 1699269694, 54724, "SRX20928872", "SRS18204809", null, null, "Children's Hospital of Capital Institute of Pediatrics", 2, 0.94793, 0.94488, 0.07407, 0.07319, 0.75493, 0.75578, 0.45437, 0.45369, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-07-06", "Undetermined", "Embryo", "Blood", "Hematopoietic System"], [76586, "SRR25181150", "SRX20928871", "SRS18204814", "SRP447851", "PRJNA991987", "RNA seq for gata1+ cells in add1 mutant zebrafish embryos and siblings at 22 hpf", "GSE236659", "Transcriptome Analysis", "Adducin 1 Add1 functions primarily as a membrane cytoskeletal protein whereas Add1 contains a bipartite nuclear localization signal implying its special nuclear function. However the nuclear functional roles of Add1 apart from maintaining cytoskeletal stability remain unknown. Here we created add1 deficient zebrafish using Tol2 transposon mediated gene trapping and evaluated how add1 deficiency affected early hematopoiesis development. When add1 is lacking in zebrafish both the primitive erythropoiesis and definitive hematopoiesis are compromised and the primitive erythroblast cells are unable to develop into healthy erythrocytes. More significantly the RNA sequencing results demonstrated that the p53 pathway is activated in the add1 depletion erythroblast cells causing the erythroblasts to undergo apoptosis at the 14 somites stage and 24 hpf. Additionally the anemic phenotype and apoptosis in add1 deficient embryos can be partially rescued by p53 insufficiency. Taken together our findings show that add1 is critical for zebrafish erythropoiesis partially through the p53 mediated apoptotic pathway which expands the regulatory role of Add1 for nuclear function. Overall design: To better understand the nuclear specific function of add1 we used RNA seq to analyze transcriptome changes in gata1 EGFP positive cells sorted from add1 deficient embryos and siblings at 22 hpf when the differences in the number of erythrocytes were not yet evident in add1 mutant embryos. Comparative gene expression profiling analysis of RNA seq data for erythroblast of add1 mutant and siblings.", null, "pubmed:37636049", null, "MT", "GSM7567235", null, "tissue:erythroblast|cell type:erythroblast|genotype:add1 knockout|geo loc name:missing|collection date:missing", "MT", "For gene expression analysis the matched reads were calculated and then normalized to RPKM using RESM software The significance of the differential expression of genes was defined by the bioinformatics service of BGI according to the combination of the absolute value of log2 Ratio \u22651 and FDR \u2264 0.001. Library construction and sequencing were performed on a BGISEQ 500. Assembly: GRCz10.81 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file include RPKM values for each Sample", "erythroblast", null, "Total RNA was isolated using SMART Seq\u00ae HT Kit. Library construction and sequencing were performed on a BGISEQ 500 by CapitalBio Technology www.capitalbiotech.com Beijin China. Clean tags were mapped to the reference genome and genes available at the Zebrafish Genome.", null, "cell type:erythroblast|genotype:add1 knockout", "GSM7567235", "GSM7567235: MT; Danio rerio; RNA Seq", "GSM7567235 r1", "GSM7567235", "1", "Total RNA was isolated using SMART Seq\u00ae HT Kit. Library construction and sequencing were performed on a BGISEQ 500 by CapitalBio Technology www.capitalbiotech.com Beijin China. Clean tags were mapped to the reference genome and genes available at the Zebrafish Genome.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP447851", null, null, "MT_1.fq.gz MT_2.fq.gz", "fastq fastq", 5929551300.0, 19765171.0, "GSM7567235 r1", "0:150 1:150", "A:1637382549;C:1315432930;G:1401397872;T:1575277995;N:59954", 150, 150, null, null, 1637382549, 1315432930, 1401397872, 1575277995, 59954, "SRX20928871", "SRS18204814", null, null, "Children's Hospital of Capital Institute of Pediatrics", 2, 0.94579, 0.94497, 0.08957, 0.08915, 0.7315, 0.7329, 0.44901, 0.45809, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-07-06", "Undetermined", "Embryo", "Blood", "Hematopoietic System"]], "truncated": false, "filtered_table_rows_count": 87, "expanded_columns": [], "expandable_columns": [], "columns": ["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", 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[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 from run_metadata where \"devstage_curation_coarse\" = :p0 and \"tissue_curation_coarse\" = :p1 order by rowid limit 101", "params": {"p0": "Embryo", "p1": "Hematopoietic System"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation_coarse=Hematopoietic+System", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 85, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&tissue_curation_coarse=Hematopoietic+System&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "miRNA-Seq", "label": "miRNA-Seq", "count": 2, "toggle_url": 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