rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse 24784,SRR25502048,SRX21232930,SRS18488024,SRP453114,PRJNA1001808,The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger,GSE239949,Transcriptome Analysis,From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.,,pubmed:28382966,,Sample 15 05316 MCK mut3,GSM7678168,,tissue:lyz+ mpx+ granulocytes|cell type:lyz+ mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf|geo loc name:missing|collection date:missing,Sample 15 05316 MCK mut3,Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample,lyz+ mpx+ granulocytes,,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.,,cell type:lyz+ mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf,GSM7678168,GSM7678168: Sample 15 05316 MCK mut3; Danio rerio; RNA Seq,GSM7678168 r1,GSM7678168,1,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP453114,,,15-05316_MCK_mut3_GTGCTT_L002_R1_001.fastq.gz 15-05316_MCK_mut3_GTGCTT_L002_R2_001.fastq.gz,fastq fastq,4329868620.0,20618422.0,GSM7678168 r1,0:105 1:105,A:1075032412;C:1077085067;G:1119735718;T:1057797736;N:217687,105,105,,,1075032412,1077085067,1119735718,1057797736,217687,SRX21232930,SRS18488024,SRA1685493,"Rural Clinical Sciences, La Trobe University","Rural Clinical Sciences, La Trobe University",2,0.78961,0.91048,0.20166,0.23232,0.81556,0.81115,0.59478,0.59379,105,105,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-08-03,Hatching,Embryo,Blood,Hematopoietic System 24785,SRR25502049,SRX21232929,SRS18488023,SRP453114,PRJNA1001808,The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger,GSE239949,Transcriptome Analysis,From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.,,pubmed:28382966,,Sample 15 05316 MCK mut2,GSM7678167,,tissue:lyz+ mpx+ granulocytes|cell type:lyz+ mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf|geo loc name:missing|collection date:missing,Sample 15 05316 MCK mut2,Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample,lyz+ mpx+ granulocytes,,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.,,cell type:lyz+ mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf,GSM7678167,GSM7678167: Sample 15 05316 MCK mut2; Danio rerio; RNA Seq,GSM7678167 r1,GSM7678167,1,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP453114,,,15-05316_MCK_mut2_ACCTCA_L002_R1_001.fastq.gz 15-05316_MCK_mut2_ACCTCA_L002_R2_001.fastq.gz,fastq fastq,4444374270.0,21163687.0,GSM7678167 r1,0:105 1:105,A:1114919906;C:1098541058;G:1145427151;T:1085262902;N:223253,105,105,,,1114919906,1098541058,1145427151,1085262902,223253,SRX21232929,SRS18488023,SRA1685493,"Rural Clinical Sciences, La Trobe University","Rural Clinical Sciences, La Trobe University",2,0.74961,0.90068,0.18596,0.22057,0.81115,0.80754,0.5829,0.58615,105,105,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-08-03,Hatching,Embryo,Blood,Hematopoietic System 24786,SRR25502050,SRX21232928,SRS18488022,SRP453114,PRJNA1001808,The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger,GSE239949,Transcriptome Analysis,From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.,,pubmed:28382966,,Sample 15 05316 MCK mut1,GSM7678166,,tissue:lyz+ mpx+ granulocytes|cell type:lyz+ mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf|geo loc name:missing|collection date:missing,Sample 15 05316 MCK mut1,Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample,lyz+ mpx+ granulocytes,,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.,,cell type:lyz+ mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf,GSM7678166,GSM7678166: Sample 15 05316 MCK mut1; Danio rerio; RNA Seq,GSM7678166 r1,GSM7678166,1,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP453114,,,15-05316_MCK_mut1_GCACTA_L002_R1_001.fastq.gz 15-05316_MCK_mut1_GCACTA_L002_R2_001.fastq.gz,fastq fastq,4459467180.0,21235558.0,GSM7678166 r1,0:105 1:105,A:1206908747;C:1012207561;G:1060393698;T:1179731376;N:225798,105,105,,,1206908747,1012207561,1060393698,1179731376,225798,SRX21232928,SRS18488022,SRA1685493,"Rural Clinical Sciences, La Trobe University","Rural Clinical Sciences, La Trobe University",2,0.75719,0.88462,0.20719,0.24095,0.78559,0.77914,0.50538,0.55691,105,105,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-08-03,Hatching,Embryo,Blood,Hematopoietic System 24787,SRR25502051,SRX21232927,SRS18488021,SRP453114,PRJNA1001808,The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger,GSE239949,Transcriptome Analysis,From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.,,pubmed:28382966,,Sample 15 05315 MCK WT3,GSM7678165,,tissue:lyz+ mpx+ granulocytes|cell type:lyz+ mpx+ granulocytes|genotype:wild type|age:48 hpf|geo loc name:missing|collection date:missing,Sample 15 05315 MCK WT3,Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample,lyz+ mpx+ granulocytes,,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.,,cell type:lyz+ mpx+ granulocytes|genotype:wild type|age:48 hpf,GSM7678165,GSM7678165: Sample 15 05315 MCK WT3; Danio rerio; RNA Seq,GSM7678165 r1,GSM7678165,1,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP453114,,,15-05315_MCK_WT3_AGTGAG_L002_R1_001.fastq.gz 15-05315_MCK_WT3_AGTGAG_L002_R2_001.fastq.gz,fastq fastq,3925329240.0,18692044.0,GSM7678165 r1,0:105 1:105,A:1022654212;C:930239389;G:973328942;T:998905803;N:200894,105,105,,,1022654212,930239389,973328942,998905803,200894,SRX21232927,SRS18488021,SRA1685493,"Rural Clinical Sciences, La Trobe University","Rural Clinical Sciences, La Trobe University",2,0.75647,0.89377,0.19165,0.22718,0.81057,0.80501,0.51173,0.54819,105,105,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-08-03,Hatching,Embryo,Blood,Hematopoietic System 24788,SRR25502052,SRX21232926,SRS18488020,SRP453114,PRJNA1001808,The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger,GSE239949,Transcriptome Analysis,From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.,,pubmed:28382966,,Sample 15 05314 MCK WT2,GSM7678164,,tissue:lyz+ mpx+ granulocytes|cell type:lyz+ mpx+ granulocytes|genotype:wild type|age:48 hpf|geo loc name:missing|collection date:missing,Sample 15 05314 MCK WT2,Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample,lyz+ mpx+ granulocytes,,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.,,cell type:lyz+ mpx+ granulocytes|genotype:wild type|age:48 hpf,GSM7678164,GSM7678164: Sample 15 05314 MCK WT2; Danio rerio; RNA Seq,GSM7678164 r1,GSM7678164,1,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP453114,,,15-05314_MCK_WT2_TGGTGA_L002_R2_001.fastq.gz 15-05314_MCK_WT2_TGGTGA_L002_R1_001.fastq.gz,fastq fastq,4100489820.0,19526142.0,GSM7678164 r1,0:105 1:105,A:1022482319;C:1016090490;G:1063619365;T:998086417;N:211229,105,105,,,1022482319,1016090490,1063619365,998086417,211229,SRX21232926,SRS18488020,SRA1685493,"Rural Clinical Sciences, La Trobe University","Rural Clinical Sciences, La Trobe University",2,0.76378,0.90522,0.20093,0.23619,0.82467,0.82049,0.57261,0.562,105,105,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-08-03,Hatching,Embryo,Blood,Hematopoietic System 24789,SRR25502053,SRX21232925,SRS18488019,SRP453114,PRJNA1001808,The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger,GSE239949,Transcriptome Analysis,From a forward genetic screen in zebrafish we identified the transcription factor ZBTB11 as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1 GFI1 and CEBPa. To better understand target genes regulated by Zbtb11 RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.,,pubmed:28382966,,Sample 15 05313 MCK WT1,GSM7678163,,tissue:lyz+ mpx+ granulocytes|cell type:lyz+ mpx+ granulocytes|genotype:wild type|age:48 hpf|geo loc name:missing|collection date:missing,Sample 15 05313 MCK WT1,Data were QC’d using FastQC ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell Victorian Bioinformatics Consortium Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample,lyz+ mpx+ granulocytes,,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.,,cell type:lyz+ mpx+ granulocytes|genotype:wild type|age:48 hpf,GSM7678163,GSM7678163: Sample 15 05313 MCK WT1; Danio rerio; RNA Seq,GSM7678163 r1,GSM7678163,1,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation followed by Ovation Ultralow System V2 for library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP453114,,,15-05313_MCK_WT1_AACCAG_L002_R1_001.fastq.gz 15-05313_MCK_WT1_AACCAG_L002_R2_001.fastq.gz,fastq fastq,4135721100.0,19693910.0,GSM7678163 r1,0:105 1:105,A:1048700719;C:1014162128;G:1070155053;T:1002495763;N:207437,105,105,,,1048700719,1014162128,1070155053,1002495763,207437,SRX21232925,SRS18488019,SRA1685493,"Rural Clinical Sciences, La Trobe University","Rural Clinical Sciences, La Trobe University",2,0.70974,0.9073,0.1771,0.22534,0.82483,0.81625,0.56311,0.55183,105,105,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-08-03,Hatching,Embryo,Blood,Hematopoietic System 25308,SRR25793380,SRX21515634,SRS18742881,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,RNA seq Erythrocytes miR 144 embryo,miR 144 embryo,,isolate:miR 144 mutant|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,Quant seq Erythrocytes miR 144 mutant Danio rerio 2 dpf replicate 3,144 3 embryo blood,144 3 embryo blood,Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457465,,,DC-144EL3_S18.fastq,fastq,687309797.0,17039739.0,DC 144EL3 S18.fastq,0:40.34,A:159186558;C:130452893;G:155820002;T:181676510;N:60173834,40,,,,159186558,130452893,155820002,181676510,60173834,SRX21515634,SRS18742881,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.52966,,0.16941,,0.97615,,0.58418,,61,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Hatching,Embryo,Blood,Hematopoietic System 25309,SRR25793381,SRX21515633,SRS18742881,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,RNA seq Erythrocytes miR 144 embryo,miR 144 embryo,,isolate:miR 144 mutant|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,Quant seq Erythrocytes miR 144 mutant Danio rerio 2 dpf replicate 2,144 2 embryo blood,144 2 embryo blood,Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457465,,,DC-144EL2_S17.fastq,fastq,495318731.0,14459195.0,DC 144EL2 S17.fastq,0:34.26,A:110392869;C:106378418;G:128881687;T:107956679;N:41709078,34,,,,110392869,106378418,128881687,107956679,41709078,SRX21515633,SRS18742881,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.32147,,0.04496,,0.97569,,0.58512,,31,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Hatching,Embryo,Blood,Hematopoietic System 25310,SRR25793382,SRX21515632,SRS18742881,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,RNA seq Erythrocytes miR 144 embryo,miR 144 embryo,,isolate:miR 144 mutant|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,Quant seq Erythrocytes miR 144 mutant Danio rerio 2 dpf replicate 1,144 1 embryo blood,144 1 embryo blood,Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457465,,,DC-144EL1_S16.fastq,fastq,974854100.0,20079553.0,DC 144EL1 S16.fastq,0:48.55,A:233861010;C:192987350;G:215192262;T:269960344;N:62853134,48,,,,233861010,192987350,215192262,269960344,62853134,SRX21515632,SRS18742881,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.77953,,0.18084,,0.90905,,0.74157,,75,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Hatching,Embryo,Blood,Hematopoietic System 25311,SRR25793383,SRX21515631,SRS18742879,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,RNA seq Erythrocytes Wild type embryo,WT embryo,,isolate:Wildtype|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,Quant seq Erythrocytes Wild type Danio rerio 2 dpf replicate 3,WT3 embryo blood,WT3 embryo blood,Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457465,,,DC-WTE3_S15.fastq,fastq,657139116.0,15618072.0,DC WTE3 S15.fastq,0:42.08,A:154495614;C:122942896;G:147719345;T:179403193;N:52578068,42,,,,154495614,122942896,147719345,179403193,52578068,SRX21515631,SRS18742879,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.56358,,0.19381,,0.96757,,0.6115,,76,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Hatching,Embryo,Blood,Hematopoietic System 25314,SRR25793386,SRX21515628,SRS18742879,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,RNA seq Erythrocytes Wild type embryo,WT embryo,,isolate:Wildtype|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,Quant seq Erythrocytes Wild type Danio rerio 2 dpf replicate 2,WT2 embryo blood,WT2 embryo blood,Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457465,,,DC-WTE2_S14.fastq,fastq,250958009.0,9755304.0,DC WTE2 S14.fastq,0:25.73,A:43225839;C:41823862;G:54150092;T:43159724;N:68598492,25,,,,43225839,41823862,54150092,43159724,68598492,SRX21515628,SRS18742879,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.34114,,0.05466,,0.96664,,0.54625,,47,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Hatching,Embryo,Blood,Hematopoietic System 25315,SRR25793387,SRX21515627,SRS18742879,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,RNA seq Erythrocytes Wild type embryo,WT embryo,,isolate:Wildtype|age:Embryo|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,Quant seq Erythrocytes Wild type Danio rerio 2 dpf replicate 1,WT1 embryo blood,WT1 embryo blood,Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457465,,,DC-WTE1_S13.fastq,fastq,816518564.0,19556325.0,DC WTE1 S13.fastq,0:41.75,A:187091550;C:151287428;G:179967901;T:221475884;N:76695801,41,,,,187091550,151287428,179967901,221475884,76695801,SRX21515627,SRS18742879,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.61681,,0.1874,,0.95101,,0.56879,,29,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Hatching,Embryo,Blood,Hematopoietic System 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.,,,,,miR 451 mutant,,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,,,,,,,,,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.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP233258,,,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,,,1795110678,2004074141,2113982350,1989843693,1399505,SRX7216663,SRS5719129,SRA1002853,University of East Anglia|Biological Sciences,University of East Anglia,1,0.97314,,0.03847,,0.81744,,0.4673,,75,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,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.,,,,,miR 144 mutant,,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,,,,,,,,,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.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP233258,,,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,,,4937891523,5429635867,5884853915,5410789187,3350857,SRX7216662,SRS5719128,SRA1002853,University of East Anglia|Biological Sciences,University of East Anglia,1,0.97729,,0.02379,,0.84102,,0.45517,,76,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,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.,,,,,wild type,,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,,,,,,,,,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.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP233258,,,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,,,1229417939,1341096472,1448568683,1339375309,775658,SRX7216661,SRS5719127,SRA1002853,University of East Anglia|Biological Sciences,University of East Anglia,1,0.97314,,0.02809,,0.83179,,0.40499,,75,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,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.,,,,,miR 144 mutant,,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,,,,,,,,,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.,,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP233258,,,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,,,,63063755,66933795,92235682,61966771,8418,SRX7216660,SRS5719128,SRA1002853,University of East Anglia|Biological Sciences,University of East Anglia,1,0.02041,,0.00444,,0.98512,,0.44771,,28,,B,,usable mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,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.,,,,,wild type,,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,,,,,,,,,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.,,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP233258,,,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,,,,65237071,85092331,80441993,63494506,9158,SRX7216659,SRS5719127,SRA1002853,University of East Anglia|Biological Sciences,University of East Anglia,1,0.00854,,0.00213,,0.99184,,0.55467,,31,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United Kingdom,2019-11-26,Hatching,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.,,,,Model organism or animal sample from Danio rerio,RNA RBC mutant rep3,,strain:gata1:dsRed transgenic line|dev stage:2 dpf|sex:not collected|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,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,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP311888,,,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,,,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,,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.,,,,Model organism or animal sample from Danio rerio,RNA RBC mutant rep2,,strain:gata1:dsRed transgenic line|dev stage:2 dpf|sex:not collected|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,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,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP311888,,,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,,,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,,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.,,,,Model organism or animal sample from Danio rerio,RNA RBC mutant rep1,,strain:gata1:dsRed transgenic line|dev stage:2 dpf|sex:not collected|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,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,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP311888,,,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,,,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,,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.,,,,Model organism or animal sample from Danio rerio,RNA RBC sibling rep3,,strain:gata1:dsRed transgenic line|dev stage:2 dpf|sex:not collected|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,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,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP311888,,,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,,,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,,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.,,,,Model organism or animal sample from Danio rerio,RNA RBC sibling rep2,,strain:gata1:dsRed transgenic line|dev stage:2 dpf|sex:not collected|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,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,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP311888,,,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,,,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,,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.,,,,Model organism or animal sample from Danio rerio,RNA RBC sibling rep1,,strain:gata1:dsRed transgenic line|dev stage:2 dpf|sex:not collected|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,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,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP311888,,,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,,,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,,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.,,pubmed:34525360,,runx1:mCherry+ at 52 hpf #2 replicate,GSM5525118,,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,,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.,,developmental stage:52 hpf line:runx1+23:nls mCherry,GSM5525118,GSM5525118: runx1:mCherry+ at 52 hpf #2 replicate; Danio rerio; RNA Seq,GSM5525118,,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,,SRP332734,,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,,6826510360,7720741166,7033747534,7231279942,844348,SRX11783413,SRS9786611,SRA1278863,GEO,"Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine",1,0.95266,,0.01784,,0.93022,,0.46235,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,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.,,pubmed:34525360,,runx1:mCherry+ at 52 hpf #2 replicate,GSM5525118,,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,,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.,,developmental stage:52 hpf line:runx1+23:nls mCherry,GSM5525118,GSM5525118: runx1:mCherry+ at 52 hpf #2 replicate; Danio rerio; RNA Seq,GSM5525118,,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,,SRP332734,,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,,7901205395,8819719149,8118311347,8243562587,5238172,SRX11783413,SRS9786611,SRA1278863,GEO,"Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine",1,0.94536,,0.018,,0.92839,,0.45489,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,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.,,pubmed:34525360,,runx1:mCherry+ at 52 hpf #1,GSM5525117,,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,,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.,,developmental stage:52 hpf line:runx1+23:nls mCherry,GSM5525117,GSM5525117: runx1:mCherry+ at 52 hpf #1; Danio rerio; RNA Seq,GSM5525117,,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,,SRP332734,,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,,7500200023,8401456631,7492567345,8038123819,929482,SRX11783412,SRS9786609,SRA1278863,GEO,"Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine",1,0.94027,,0.01204,,0.94107,,0.46801,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,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.,,pubmed:34525360,,runx1:mCherry+ at 52 hpf #1,GSM5525117,,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,,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.,,developmental stage:52 hpf line:runx1+23:nls mCherry,GSM5525117,GSM5525117: runx1:mCherry+ at 52 hpf #1; Danio rerio; RNA Seq,GSM5525117,,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,,SRP332734,,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,,7164346674,7911114850,7135136885,7555336618,4753823,SRX11783412,SRS9786609,SRA1278863,GEO,"Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine",1,0.93152,,0.01164,,0.94152,,0.46255,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,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.,,pubmed:34525360,,draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate,GSM5525116,,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,,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.,,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,,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,,SRP332734,,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,,6786904201,7461082970,6741279762,7286929534,827033,SRX11783411,SRS9786608,SRA1278863,GEO,"Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine",1,0.9442,,0.02532,,0.92577,,0.45185,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,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.,,pubmed:34525360,,draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate,GSM5525116,,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,,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.,,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,,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,,SRP332734,,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,,8422157482,9164931651,8346143692,8946552575,4472750,SRX11783411,SRS9786608,SRA1278863,GEO,"Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine",1,0.93666,,0.02678,,0.92232,,0.44942,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,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.,,pubmed:34525360,,draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate,GSM5525116,,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,,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.,,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,,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,,SRP332734,,,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,,,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,,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.,,pubmed:34525360,,draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate,GSM5525116,,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,,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.,,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,,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,,SRP332734,,,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,,,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,,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.,,pubmed:34525360,,draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate,GSM5525116,,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,,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.,,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,,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,,SRP332734,,,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,,,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,,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.,,pubmed:34525360,,draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate,GSM5525116,,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,,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.,,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,,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,,SRP332734,,,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,,,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,,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.,,pubmed:34525360,,draculin:mCherry+;gata1:GFP at 52 hpf #1,GSM5525115,,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,,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.,,developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,GSM5525115,GSM5525115: draculin:mCherry+;gata1:GFP at 52 hpf #1; Danio rerio; RNA Seq,GSM5525115,,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,,SRP332734,,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,,6268319263,6935405810,6236287882,6768309909,777686,SRX11783410,SRS9786606,SRA1278863,GEO,"Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine",1,0.94373,,0.02418,,0.93206,,0.4538,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,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.,,pubmed:34525360,,draculin:mCherry+;gata1:GFP at 52 hpf #1,GSM5525115,,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,,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.,,developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,GSM5525115,GSM5525115: draculin:mCherry+;gata1:GFP at 52 hpf #1; Danio rerio; RNA Seq,GSM5525115,,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,,SRP332734,,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,,6636746214,7271043747,6588518102,7092648593,3585944,SRX11783410,SRS9786606,SRA1278863,GEO,"Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine",1,0.9348,,0.02385,,0.93156,,0.45273,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,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.,,pubmed:34525360,,draculin:mCherry+;gata1:GFP at 52 hpf #1,GSM5525115,,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,,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.,,developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,GSM5525115,GSM5525115: draculin:mCherry+;gata1:GFP at 52 hpf #1; Danio rerio; RNA Seq,GSM5525115,,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,,SRP332734,,,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,,,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,,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.,,pubmed:34525360,,draculin:mCherry+;gata1:GFP at 52 hpf #1,GSM5525115,,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,,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.,,developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,GSM5525115,GSM5525115: draculin:mCherry+;gata1:GFP at 52 hpf #1; Danio rerio; RNA Seq,GSM5525115,,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,,SRP332734,,,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,,,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,,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.,,pubmed:34525360,,draculin:mCherry+;gata1:GFP at 52 hpf #1,GSM5525115,,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,,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.,,developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,GSM5525115,GSM5525115: draculin:mCherry+;gata1:GFP at 52 hpf #1; Danio rerio; RNA Seq,GSM5525115,,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,,SRP332734,,,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,,,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,,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.,,pubmed:34525360,,draculin:mCherry+;gata1:GFP at 52 hpf #1,GSM5525115,,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,,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.,,developmental stage:52 hpf line:draculin:mCherry;gata1:GFP,GSM5525115,GSM5525115: draculin:mCherry+;gata1:GFP at 52 hpf #1; Danio rerio; RNA Seq,GSM5525115,,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,,SRP332734,,,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,,,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,,United States,2021-08-16,Hatching,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.,,pubmed:38326409,,Tgmpx:eGFP 2,GSM7506191,,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 μg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS® 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.,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 μg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS® 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP445421,,,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,,,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,,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.,,pubmed:38326409,,Tgmpx:eGFP 1,GSM7506190,,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 μg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS® 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.,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 μg total RNA was used for following library preparation. Paired end libraries were prepared using the VAHTS® 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP445421,,,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,,,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,,China,2023-06-22,Hatching,Embryo,Blood,Hematopoietic System