{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Segmentation\" and tissue_curation = \"Trunk\"", "rows": [[48629, "SRR7280656", "SRX4184226", "SRS3395606", "SRP149913", "PRJNA474911", "Origin and Evolution of Neural Microexons", "PRJNA474911", "Other", "Our study focuses on the origin of the neural microexon program.We discover that neural microexon programs are present in non vertebrate speciesand trace their origin to bilaterian ancestors through the emergenceof a previously uncharacterized \"enhancer of microexon\" eMIC protein domain", null, null, "Pool of one hundred 12hpf embryos", "12hpf embryos", "Embr 12hpf", null, "strain:AB|dev stage:12hpf|sex:pooled male and female|tissue:whole body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: 12hpf embryos", "Embr 12hpf", "Embr 12hpf", "RNA extracted from a pool of one hundred embryos", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP149913", null, null, "Embr_12hpf_R2-125.fq.gz Embr_12hpf_R1-125.fq.gz", "fastq fastq", 22366284500.0, 89465138.0, "Embr 12hpf R1 125.fq.gz", "0:125 1:125", "A:5886492098;C:5284016845;G:5382041408;T:5809628253;N:4105896", 125, 125, null, null, 5886492098, 5284016845, 5382041408, 5809628253, 4105896, "SRX4184226", "SRS3395606", "SRA717220", "Centre for Genomic Regulation|Systems Biology Department", "Centre for Genomic Regulation", 2, 0.96226, 0.96763, 0.06393, 0.06451, 0.74355, 0.74472, 0.48233, 0.48387, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2019-01-22", "Segmentation", "Embryo", "Trunk", "Surface Structure"], [62669, "SRR13269771", "SRX9699908", "SRS7895936", "SRP298388", "PRJNA686152", "Transcriptionally regulated energy metabolism drives early erythropoiesis mon RNA seq", "GSE163454", "Transcriptome Analysis", "Transcription and metabolism both influence cell function yet dedicated transcriptional control of metabolic pathways that regulate cell fate has rarely been defined. Through a chemical suppressor screen  we discovered that inhibition of the pyrimidine biosynthesis enzyme DHODH rescues erythroid differentiation in bloodless moonshine mutant embryos defective for the transcription elongation factor tif1?. This rescue depends on the functional link of DHODH to mitochondrial respiration. Low a ketoglutarate levels caused by tif1? loss lead to histone hypermethylation. TIF? directly controls coenzyme Q synthesis gene expression and coenzyme Q levels are reduced in moonshine mutants. A coenzyme Q analogue rescues moonshine's bloodless phenotype. These results demonstrate mitochondrial metabolism is a key output of a lineage transcription factor that drives cell fate decisions in the early blood lineage. Overall design: Heterozygous mon;drl:eGFP fish were crossed with heterozygous mon fish  ensuring transmission of only one allele of drl:EGFP and embryos sorted for green fluorescence which is markedly reduced in mon mutant embryos beginning at 21 hpf. 30 phenotypically mon and wild type embryos were harvested per replicate = clutch  each clutch from one pairwise mating for RNA seq by homogenizing in TRIzol.", "parent bioproject:PRJNA562552", "pubmed:33986176", null, "wild type/het clutch 13 at 22 hpf", "GSM4979521", null, "source name:Whole zebrafish embryos at 22 hpf|tissue:Whole body|genotype/variation:wild type/het|developmental stage:22 hpf|clutch:13", "wild type/het clutch 13 at 22 hpf", "Step 1: Quality control of RNA Seq datasets was performed by FastQC and Cutadapt to remove adaptor sequences and low quality regions. Step 2: The high quality reads were aligned to Ensembl genome assembly GRCz11 using Tophat 2.0.11 without xxx splicing form calls. Step 3: Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. Step 4: FPKM values were used to normalize and quantify each transcripts; the resulting list of differential expressed genes are filtered by log2 fold change > 2 and q value < 0.05. Genome build: Ensembl GRCz11 Supplementary files format and content: 30 426592019.htseq count.out.txt: Fragments Per Kilobase of transcript per Million mapped reads FPKM files contain gene names and FPKM values.", "Whole zebrafish embryos at 22 hpf", "No treatment.", "post thawing the samples  each with 30 embryos per phenotype and time point in triplicate homogenized in 500 \u00b5l TRIzol Invitrogen/Thermo Fisher Scientific  15596026  samples were transferred into a pre spun 16 000 x g  30 s  room temperature 2 ml 5PRIME Phase Lock Gel Heavy tube Quantabio  2302830. post addition of 100 \u00b5l chloroform Sigma Aldrich  C2432  the tube was vigorously inverted for 15 sec  incubated at room temperature for 3 min and spun at 12 000 x g for 15 min at 4\u00b0C. The supernatant was transferred into a RNase free 1.7 ml tube. 150 \u00b5l buffer saturated phenol Invitrogen/Thermo Fisher Scientific  15513039 and 150 \u00b5l chloroform were added  the samples vortexed for 15 sec  and incubated and spun as before. The supernatant was transferred into a fresh RNase free 1.7 ml tube  300 \u00b5l chloroform added  the samples were vortexed  incubated and spun as before. The supernatant was transferred into a fresh RNase free 1.7 ml tube  250 \u00b5l 2 propanol VWR  BDH1133 added  the samples were inverted 10 times  samples were spun at 17 000 x g for 10 min at 4\u00b0C  and the supernatant was pipetted off. Samples were handled on ice from now on. Samples were washed three times with 1000 \u00b5l 75% ethanol in nuclease free water Invitrogen/Thermo Fisher Scientific  AM9937 followed by spinning at 17 000 x g for 5 min at 4\u00b0C. post the final wash  samples were air dried and resuspended in 50 \u00b5l nuclease free water. 5 \u00b5g of RNA was DNase treated with the TURBO DNA free Kit Ambion  AM1907 as per the manufacturer\u2019s protocol  in a volume of 50 \u00b5l for 30 min at 37\u00b0C. Instead of adding the DNase Inactivation Reagent  the reaction was cleaned up using RNAClean XP SPRI paramagnetic beads Beckman Coulter  A63987 following the manufacturer\u2019s instructions. The final elution volume was 28 \u00b5l. 1 \u00b5g DNase treated RNA samples were spiked with ERCC ExFold RNA Spike In Mixes Thermo Fisher Scientific  4456739 as per the manufacturer\u2019s protocol. Ribosomal RNAs were removed with the NEBNext rRNA Depletion Kit v2 NEB  E7400  followed by a clean up with RNAClean XP SPRI paramagnetic beads Beckman Coulter  A63987. Strand specific libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB E7760 and NEBNext Multiplex Oligos for Illumina NEB  E7335  all according to the manufacturer\u2019s protocols. For quality control and pooling purposes  the final libraries were run on a HS D1000 ScreenTape in the Agilent 2200 TapeStation System. The average library size was 278 bp. Libraries were sequenced on the Illumina HiSeq 4000.", "Zebrafish embryos were grown in embryo medium E3 at 28.5\u00b0C water temperature as per standard protocols.", "tissue:Whole body|genotype/variation:wild type/het|developmental stage:22 hpf|clutch:13", "GSM4979521", "GSM4979521: wild type/het clutch 13 at 22 hpf; Danio rerio; RNA Seq", "GSM4979521", null, "1", "post thawing the samples  each with 30 embryos per phenotype and time point in triplicate homogenized in 500 \u00b5l TRIzol Invitrogen/Thermo Fisher Scientific  15596026  samples were transferred into a pre spun 16 000 x g  30 s  room temperature 2 ml 5PRIME Phase Lock Gel Heavy tube Quantabio  2302830. post addition of 100 \u00b5l chloroform Sigma Aldrich  C2432  the tube was vigorously inverted for 15 sec  incubated at room temperature for 3 min and spun at 12 000 x g for 15 min at 4\u00b0C. The supernatant was transferred into a RNase free 1.7 ml tube. 150 \u00b5l buffer saturated phenol Invitrogen/Thermo Fisher Scientific  15513039 and 150 \u00b5l chloroform were added  the samples vortexed for 15 sec  and incubated and spun as before. The supernatant was transferred into a fresh RNase free 1.7 ml tube  300 \u00b5l chloroform added  the samples were vortexed  incubated and spun as before. The supernatant was transferred into a fresh RNase free 1.7 ml tube  250 \u00b5l 2 propanol VWR  BDH1133 added  the samples were inverted 10 times  samples were spun at 17 000 x g for 10 min at 4\u00b0C  and the supernatant was pipetted off. Samples were handled on ice from now on. Samples were washed three times with 1000 \u00b5l 75% ethanol in nuclease free water Invitrogen/Thermo Fisher Scientific  AM9937 followed by spinning at 17 000 x g for 5 min at 4\u00b0C. post the final wash  samples were air dried and resuspended in 50 \u00b5l nuclease free water. 5 \u00b5g of RNA was DNase treated with the TURBO DNA free Kit Ambion  AM1907 as per the manufacturer's protocol  in a volume of 50 \u00b5l for 30 min at 37\u00b0C. Instead of adding the DNase Inactivation Reagent  the reaction was cleaned up using RNAClean XP SPRI paramagnetic beads Beckman Coulter  A63987 following the manufacturer's instructions. The final elution volume was 28 \u00b5l. 1 \u00b5g DNase treated RNA samples were spiked with ERCC ExFold RNA Spike In Mixes Thermo Fisher Scientific  4456739 as per the manufacturer's protocol. Ribosomal RNAs were removed with the NEBNext rRNA Depletion Kit v2 NEB  E7400  followed by a clean up with RNAClean XP SPRI paramagnetic beads Beckman Coulter  A63987. Strand specific libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB E7760 and NEBNext Multiplex Oligos for Illumina NEB  E7335  all according to the manufacturer's protocols. For quality control and pooling purposes  the final libraries were run on a HS D1000 ScreenTape in the Agilent 2200 TapeStation System. The average library size was 278 bp. Libraries were sequenced on the Illumina HiSeq 4000.", "GEO Accession:GSM4979521", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP298388", null, null, "MR-9_R1_001.fastq.gz MR-9_R2_001.fastq.gz", "fastq fastq", 11544716100.0, 38482387.0, "GSM4979521 r1", "0:150 1:150", "A:2493178821;C:3257070138;G:3383701180;T:2409010235;N:1755726", 150, 150, null, null, 2493178821, 3257070138, 3383701180, 2409010235, 1755726, "SRX9699908", "SRS7895936", "SRA1174486", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.93785, 0.94472, 0.22238, 0.22075, 0.75459, 0.7615, 0.75403, 0.74823, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2020-12-17", "Segmentation", "Embryo", "Trunk", "Surface Structure"], [62670, "SRR13269770", "SRX9699907", "SRS7895935", "SRP298388", "PRJNA686152", "Transcriptionally regulated energy metabolism drives early erythropoiesis mon RNA seq", "GSE163454", "Transcriptome Analysis", "Transcription and metabolism both influence cell function yet dedicated transcriptional control of metabolic pathways that regulate cell fate has rarely been defined. Through a chemical suppressor screen  we discovered that inhibition of the pyrimidine biosynthesis enzyme DHODH rescues erythroid differentiation in bloodless moonshine mutant embryos defective for the transcription elongation factor tif1?. This rescue depends on the functional link of DHODH to mitochondrial respiration. Low a ketoglutarate levels caused by tif1? loss lead to histone hypermethylation. TIF? directly controls coenzyme Q synthesis gene expression and coenzyme Q levels are reduced in moonshine mutants. A coenzyme Q analogue rescues moonshine's bloodless phenotype. These results demonstrate mitochondrial metabolism is a key output of a lineage transcription factor that drives cell fate decisions in the early blood lineage. Overall design: Heterozygous mon;drl:eGFP fish were crossed with heterozygous mon fish  ensuring transmission of only one allele of drl:EGFP and embryos sorted for green fluorescence which is markedly reduced in mon mutant embryos beginning at 21 hpf. 30 phenotypically mon and wild type embryos were harvested per replicate = clutch  each clutch from one pairwise mating for RNA seq by homogenizing in TRIzol.", "parent bioproject:PRJNA562552", "pubmed:33986176", null, "wild type/het clutch 11 at 22 hpf", "GSM4979520", null, "source name:Whole zebrafish embryos at 22 hpf|tissue:Whole body|genotype/variation:wild type/het|developmental stage:22 hpf|clutch:11", "wild type/het clutch 11 at 22 hpf", "Step 1: Quality control of RNA Seq datasets was performed by FastQC and Cutadapt to remove adaptor sequences and low quality regions. Step 2: The high quality reads were aligned to Ensembl genome assembly GRCz11 using Tophat 2.0.11 without xxx splicing form calls. Step 3: Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. Step 4: FPKM values were used to normalize and quantify each transcripts; the resulting list of differential expressed genes are filtered by log2 fold change > 2 and q value < 0.05. Genome build: Ensembl GRCz11 Supplementary files format and content: 30 426592019.htseq count.out.txt: Fragments Per Kilobase of transcript per Million mapped reads FPKM files contain gene names and FPKM values.", "Whole zebrafish embryos at 22 hpf", "No treatment.", "post thawing the samples  each with 30 embryos per phenotype and time point in triplicate homogenized in 500 \u00b5l TRIzol Invitrogen/Thermo Fisher Scientific  15596026  samples were transferred into a pre spun 16 000 x g  30 s  room temperature 2 ml 5PRIME Phase Lock Gel Heavy tube Quantabio  2302830. post addition of 100 \u00b5l chloroform Sigma Aldrich  C2432  the tube was vigorously inverted for 15 sec  incubated at room temperature for 3 min and spun at 12 000 x g for 15 min at 4\u00b0C. The supernatant was transferred into a RNase free 1.7 ml tube. 150 \u00b5l buffer saturated phenol Invitrogen/Thermo Fisher Scientific  15513039 and 150 \u00b5l chloroform were added  the samples vortexed for 15 sec  and incubated and spun as before. The supernatant was transferred into a fresh RNase free 1.7 ml tube  300 \u00b5l chloroform added  the samples were vortexed  incubated and spun as before. The supernatant was transferred into a fresh RNase free 1.7 ml tube  250 \u00b5l 2 propanol VWR  BDH1133 added  the samples were inverted 10 times  samples were spun at 17 000 x g for 10 min at 4\u00b0C  and the supernatant was pipetted off. Samples were handled on ice from now on. Samples were washed three times with 1000 \u00b5l 75% ethanol in nuclease free water Invitrogen/Thermo Fisher Scientific  AM9937 followed by spinning at 17 000 x g for 5 min at 4\u00b0C. post the final wash  samples were air dried and resuspended in 50 \u00b5l nuclease free water. 5 \u00b5g of RNA was DNase treated with the TURBO DNA free Kit Ambion  AM1907 as per the manufacturer\u2019s protocol  in a volume of 50 \u00b5l for 30 min at 37\u00b0C. Instead of adding the DNase Inactivation Reagent  the reaction was cleaned up using RNAClean XP SPRI paramagnetic beads Beckman Coulter  A63987 following the manufacturer\u2019s instructions. The final elution volume was 28 \u00b5l. 1 \u00b5g DNase treated RNA samples were spiked with ERCC ExFold RNA Spike In Mixes Thermo Fisher Scientific  4456739 as per the manufacturer\u2019s protocol. Ribosomal RNAs were removed with the NEBNext rRNA Depletion Kit v2 NEB  E7400  followed by a clean up with RNAClean XP SPRI paramagnetic beads Beckman Coulter  A63987. Strand specific libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB E7760 and NEBNext Multiplex Oligos for Illumina NEB  E7335  all according to the manufacturer\u2019s protocols. For quality control and pooling purposes  the final libraries were run on a HS D1000 ScreenTape in the Agilent 2200 TapeStation System. The average library size was 278 bp. Libraries were sequenced on the Illumina HiSeq 4000.", "Zebrafish embryos were grown in embryo medium E3 at 28.5\u00b0C water temperature as per standard protocols.", "tissue:Whole body|genotype/variation:wild type/het|developmental stage:22 hpf|clutch:11", "GSM4979520", "GSM4979520: wild type/het clutch 11 at 22 hpf; Danio rerio; RNA Seq", "GSM4979520", null, "1", "post thawing the samples  each with 30 embryos per phenotype and time point in triplicate homogenized in 500 \u00b5l TRIzol Invitrogen/Thermo Fisher Scientific  15596026  samples were transferred into a pre spun 16 000 x g  30 s  room temperature 2 ml 5PRIME Phase Lock Gel Heavy tube Quantabio  2302830. post addition of 100 \u00b5l chloroform Sigma Aldrich  C2432  the tube was vigorously inverted for 15 sec  incubated at room temperature for 3 min and spun at 12 000 x g for 15 min at 4\u00b0C. The supernatant was transferred into a RNase free 1.7 ml tube. 150 \u00b5l buffer saturated phenol Invitrogen/Thermo Fisher Scientific  15513039 and 150 \u00b5l chloroform were added  the samples vortexed for 15 sec  and incubated and spun as before. The supernatant was transferred into a fresh RNase free 1.7 ml tube  300 \u00b5l chloroform added  the samples were vortexed  incubated and spun as before. The supernatant was transferred into a fresh RNase free 1.7 ml tube  250 \u00b5l 2 propanol VWR  BDH1133 added  the samples were inverted 10 times  samples were spun at 17 000 x g for 10 min at 4\u00b0C  and the supernatant was pipetted off. Samples were handled on ice from now on. Samples were washed three times with 1000 \u00b5l 75% ethanol in nuclease free water Invitrogen/Thermo Fisher Scientific  AM9937 followed by spinning at 17 000 x g for 5 min at 4\u00b0C. post the final wash  samples were air dried and resuspended in 50 \u00b5l nuclease free water. 5 \u00b5g of RNA was DNase treated with the TURBO DNA free Kit Ambion  AM1907 as per the manufacturer's protocol  in a volume of 50 \u00b5l for 30 min at 37\u00b0C. Instead of adding the DNase Inactivation Reagent  the reaction was cleaned up using RNAClean XP SPRI paramagnetic beads Beckman Coulter  A63987 following the manufacturer's instructions. The final elution volume was 28 \u00b5l. 1 \u00b5g DNase treated RNA samples were spiked with ERCC ExFold RNA Spike In Mixes Thermo Fisher Scientific  4456739 as per the manufacturer's protocol. Ribosomal RNAs were removed with the NEBNext rRNA Depletion Kit v2 NEB  E7400  followed by a clean up with RNAClean XP SPRI paramagnetic beads Beckman Coulter  A63987. Strand specific libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB E7760 and NEBNext Multiplex Oligos for Illumina NEB  E7335  all according to the manufacturer's protocols. For quality control and pooling purposes  the final libraries were run on a HS D1000 ScreenTape in the Agilent 2200 TapeStation System. The average library size was 278 bp. Libraries were sequenced on the Illumina HiSeq 4000.", "GEO Accession:GSM4979520", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP298388", null, null, "MR-8_R1_001.fastq.gz MR-8_R2_001.fastq.gz", "fastq fastq", 11937285900.0, 39790953.0, "GSM4979520 r1", "0:150 1:150", "A:2590342277;C:3356480791;G:3487075346;T:2501557753;N:1829733", 150, 150, null, null, 2590342277, 3356480791, 3487075346, 2501557753, 1829733, "SRX9699907", "SRS7895935", "SRA1174486", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.93653, 0.94484, 0.22394, 0.22396, 0.7557, 0.76236, 0.74189, 0.73324, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2020-12-17", "Segmentation", "Embryo", "Trunk", "Surface Structure"], [62671, "SRR13269769", "SRX9699906", "SRS7895934", "SRP298388", "PRJNA686152", "Transcriptionally regulated energy metabolism drives early erythropoiesis mon RNA seq", "GSE163454", "Transcriptome Analysis", "Transcription and metabolism both influence cell function yet dedicated transcriptional control of metabolic pathways that regulate cell fate has rarely been defined. Through a chemical suppressor screen  we discovered that inhibition of the pyrimidine biosynthesis enzyme DHODH rescues erythroid differentiation in bloodless moonshine mutant embryos defective for the transcription elongation factor tif1?. This rescue depends on the functional link of DHODH to mitochondrial respiration. Low a ketoglutarate levels caused by tif1? loss lead to histone hypermethylation. TIF? directly controls coenzyme Q synthesis gene expression and coenzyme Q levels are reduced in moonshine mutants. A coenzyme Q analogue rescues moonshine's bloodless phenotype. These results demonstrate mitochondrial metabolism is a key output of a lineage transcription factor that drives cell fate decisions in the early blood lineage. Overall design: Heterozygous mon;drl:eGFP fish were crossed with heterozygous mon fish  ensuring transmission of only one allele of drl:EGFP and embryos sorted for green fluorescence which is markedly reduced in mon mutant embryos beginning at 21 hpf. 30 phenotypically mon and wild type embryos were harvested per replicate = clutch  each clutch from one pairwise mating for RNA seq by homogenizing in TRIzol.", "parent bioproject:PRJNA562552", "pubmed:33986176", null, "wild type/het clutch 9 at 22 hpf", "GSM4979519", null, "source name:Whole zebrafish embryos at 22 hpf|tissue:Whole body|genotype/variation:wild type/het|developmental stage:22 hpf|clutch:9", "wild type/het clutch 9 at 22 hpf", "Step 1: Quality control of RNA Seq datasets was performed by FastQC and Cutadapt to remove adaptor sequences and low quality regions. Step 2: The high quality reads were aligned to Ensembl genome assembly GRCz11 using Tophat 2.0.11 without xxx splicing form calls. Step 3: Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. Step 4: FPKM values were used to normalize and quantify each transcripts; the resulting list of differential expressed genes are filtered by log2 fold change > 2 and q value < 0.05. Genome build: Ensembl GRCz11 Supplementary files format and content: 30 426592019.htseq count.out.txt: Fragments Per Kilobase of transcript per Million mapped reads FPKM files contain gene names and FPKM values.", "Whole zebrafish embryos at 22 hpf", "No treatment.", "post thawing the samples  each with 30 embryos per phenotype and time point in triplicate homogenized in 500 \u00b5l TRIzol Invitrogen/Thermo Fisher Scientific  15596026  samples were transferred into a pre spun 16 000 x g  30 s  room temperature 2 ml 5PRIME Phase Lock Gel Heavy tube Quantabio  2302830. post addition of 100 \u00b5l chloroform Sigma Aldrich  C2432  the tube was vigorously inverted for 15 sec  incubated at room temperature for 3 min and spun at 12 000 x g for 15 min at 4\u00b0C. The supernatant was transferred into a RNase free 1.7 ml tube. 150 \u00b5l buffer saturated phenol Invitrogen/Thermo Fisher Scientific  15513039 and 150 \u00b5l chloroform were added  the samples vortexed for 15 sec  and incubated and spun as before. The supernatant was transferred into a fresh RNase free 1.7 ml tube  300 \u00b5l chloroform added  the samples were vortexed  incubated and spun as before. The supernatant was transferred into a fresh RNase free 1.7 ml tube  250 \u00b5l 2 propanol VWR  BDH1133 added  the samples were inverted 10 times  samples were spun at 17 000 x g for 10 min at 4\u00b0C  and the supernatant was pipetted off. Samples were handled on ice from now on. Samples were washed three times with 1000 \u00b5l 75% ethanol in nuclease free water Invitrogen/Thermo Fisher Scientific  AM9937 followed by spinning at 17 000 x g for 5 min at 4\u00b0C. post the final wash  samples were air dried and resuspended in 50 \u00b5l nuclease free water. 5 \u00b5g of RNA was DNase treated with the TURBO DNA free Kit Ambion  AM1907 as per the manufacturer\u2019s protocol  in a volume of 50 \u00b5l for 30 min at 37\u00b0C. Instead of adding the DNase Inactivation Reagent  the reaction was cleaned up using RNAClean XP SPRI paramagnetic beads Beckman Coulter  A63987 following the manufacturer\u2019s instructions. The final elution volume was 28 \u00b5l. 1 \u00b5g DNase treated RNA samples were spiked with ERCC ExFold RNA Spike In Mixes Thermo Fisher Scientific  4456739 as per the manufacturer\u2019s protocol. Ribosomal RNAs were removed with the NEBNext rRNA Depletion Kit v2 NEB  E7400  followed by a clean up with RNAClean XP SPRI paramagnetic beads Beckman Coulter  A63987. Strand specific libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB E7760 and NEBNext Multiplex Oligos for Illumina NEB  E7335  all according to the manufacturer\u2019s protocols. For quality control and pooling purposes  the final libraries were run on a HS D1000 ScreenTape in the Agilent 2200 TapeStation System. The average library size was 278 bp. Libraries were sequenced on the Illumina HiSeq 4000.", "Zebrafish embryos were grown in embryo medium E3 at 28.5\u00b0C water temperature as per standard protocols.", "tissue:Whole body|genotype/variation:wild type/het|developmental stage:22 hpf|clutch:9", "GSM4979519", "GSM4979519: wild type/het clutch 9 at 22 hpf; Danio rerio; RNA Seq", "GSM4979519", null, "1", "post thawing the samples  each with 30 embryos per phenotype and time point in triplicate homogenized in 500 \u00b5l TRIzol Invitrogen/Thermo Fisher Scientific  15596026  samples were transferred into a pre spun 16 000 x g  30 s  room temperature 2 ml 5PRIME Phase Lock Gel Heavy tube Quantabio  2302830. post addition of 100 \u00b5l chloroform Sigma Aldrich  C2432  the tube was vigorously inverted for 15 sec  incubated at room temperature for 3 min and spun at 12 000 x g for 15 min at 4\u00b0C. The supernatant was transferred into a RNase free 1.7 ml tube. 150 \u00b5l buffer saturated phenol Invitrogen/Thermo Fisher Scientific  15513039 and 150 \u00b5l chloroform were added  the samples vortexed for 15 sec  and incubated and spun as before. The supernatant was transferred into a fresh RNase free 1.7 ml tube  300 \u00b5l chloroform added  the samples were vortexed  incubated and spun as before. The supernatant was transferred into a fresh RNase free 1.7 ml tube  250 \u00b5l 2 propanol VWR  BDH1133 added  the samples were inverted 10 times  samples were spun at 17 000 x g for 10 min at 4\u00b0C  and the supernatant was pipetted off. Samples were handled on ice from now on. Samples were washed three times with 1000 \u00b5l 75% ethanol in nuclease free water Invitrogen/Thermo Fisher Scientific  AM9937 followed by spinning at 17 000 x g for 5 min at 4\u00b0C. post the final wash  samples were air dried and resuspended in 50 \u00b5l nuclease free water. 5 \u00b5g of RNA was DNase treated with the TURBO DNA free Kit Ambion  AM1907 as per the manufacturer's protocol  in a volume of 50 \u00b5l for 30 min at 37\u00b0C. Instead of adding the DNase Inactivation Reagent  the reaction was cleaned up using RNAClean XP SPRI paramagnetic beads Beckman Coulter  A63987 following the manufacturer's instructions. The final elution volume was 28 \u00b5l. 1 \u00b5g DNase treated RNA samples were spiked with ERCC ExFold RNA Spike In Mixes Thermo Fisher Scientific  4456739 as per the manufacturer's protocol. Ribosomal RNAs were removed with the NEBNext rRNA Depletion Kit v2 NEB  E7400  followed by a clean up with RNAClean XP SPRI paramagnetic beads Beckman Coulter  A63987. Strand specific libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB E7760 and NEBNext Multiplex Oligos for Illumina NEB  E7335  all according to the manufacturer's protocols. For quality control and pooling purposes  the final libraries were run on a HS D1000 ScreenTape in the Agilent 2200 TapeStation System. The average library size was 278 bp. Libraries were sequenced on the Illumina HiSeq 4000.", "GEO Accession:GSM4979519", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP298388", null, null, "MR-7_R1_001.fastq.gz MR-7_R2_001.fastq.gz", "fastq fastq", 11984052600.0, 39946842.0, "GSM4979519 r1", "0:150 1:150", "A:2583599261;C:3389979529;G:3513816945;T:2494827555;N:1829310", 150, 150, null, null, 2583599261, 3389979529, 3513816945, 2494827555, 1829310, "SRX9699906", "SRS7895934", "SRA1174486", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.93597, 0.94508, 0.2214, 0.22135, 0.75789, 0.76508, 0.75097, 0.73605, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2020-12-17", "Segmentation", "Embryo", "Trunk", "Surface Structure"], [62675, "SRR13269765", "SRX9699902", "SRS7895931", "SRP298388", "PRJNA686152", "Transcriptionally regulated energy metabolism drives early erythropoiesis mon RNA seq", "GSE163454", "Transcriptome Analysis", "Transcription and metabolism both influence cell function yet dedicated transcriptional control of metabolic pathways that regulate cell fate has rarely been defined. Through a chemical suppressor screen  we discovered that inhibition of the pyrimidine biosynthesis enzyme DHODH rescues erythroid differentiation in bloodless moonshine mutant embryos defective for the transcription elongation factor tif1?. This rescue depends on the functional link of DHODH to mitochondrial respiration. Low a ketoglutarate levels caused by tif1? loss lead to histone hypermethylation. TIF? directly controls coenzyme Q synthesis gene expression and coenzyme Q levels are reduced in moonshine mutants. A coenzyme Q analogue rescues moonshine's bloodless phenotype. These results demonstrate mitochondrial metabolism is a key output of a lineage transcription factor that drives cell fate decisions in the early blood lineage. Overall design: Heterozygous mon;drl:eGFP fish were crossed with heterozygous mon fish  ensuring transmission of only one allele of drl:EGFP and embryos sorted for green fluorescence which is markedly reduced in mon mutant embryos beginning at 21 hpf. 30 phenotypically mon and wild type embryos were harvested per replicate = clutch  each clutch from one pairwise mating for RNA seq by homogenizing in TRIzol.", "parent bioproject:PRJNA562552", "pubmed:33986176", null, "mon clutch 13 at 22 hpf", "GSM4979515", null, "source name:Whole zebrafish embryos at 22 hpf|tissue:Whole body|genotype/variation:mon|developmental stage:22 hpf|clutch:13", "mon clutch 13 at 22 hpf", "Step 1: Quality control of RNA Seq datasets was performed by FastQC and Cutadapt to remove adaptor sequences and low quality regions. Step 2: The high quality reads were aligned to Ensembl genome assembly GRCz11 using Tophat 2.0.11 without xxx splicing form calls. Step 3: Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. Step 4: FPKM values were used to normalize and quantify each transcripts; the resulting list of differential expressed genes are filtered by log2 fold change > 2 and q value < 0.05. Genome build: Ensembl GRCz11 Supplementary files format and content: 30 426592019.htseq count.out.txt: Fragments Per Kilobase of transcript per Million mapped reads FPKM files contain gene names and FPKM values.", "Whole zebrafish embryos at 22 hpf", "No treatment.", "post thawing the samples  each with 30 embryos per phenotype and time point in triplicate homogenized in 500 \u00b5l TRIzol Invitrogen/Thermo Fisher Scientific  15596026  samples were transferred into a pre spun 16 000 x g  30 s  room temperature 2 ml 5PRIME Phase Lock Gel Heavy tube Quantabio  2302830. post addition of 100 \u00b5l chloroform Sigma Aldrich  C2432  the tube was vigorously inverted for 15 sec  incubated at room temperature for 3 min and spun at 12 000 x g for 15 min at 4\u00b0C. The supernatant was transferred into a RNase free 1.7 ml tube. 150 \u00b5l buffer saturated phenol Invitrogen/Thermo Fisher Scientific  15513039 and 150 \u00b5l chloroform were added  the samples vortexed for 15 sec  and incubated and spun as before. The supernatant was transferred into a fresh RNase free 1.7 ml tube  300 \u00b5l chloroform added  the samples were vortexed  incubated and spun as before. The supernatant was transferred into a fresh RNase free 1.7 ml tube  250 \u00b5l 2 propanol VWR  BDH1133 added  the samples were inverted 10 times  samples were spun at 17 000 x g for 10 min at 4\u00b0C  and the supernatant was pipetted off. Samples were handled on ice from now on. Samples were washed three times with 1000 \u00b5l 75% ethanol in nuclease free water Invitrogen/Thermo Fisher Scientific  AM9937 followed by spinning at 17 000 x g for 5 min at 4\u00b0C. post the final wash  samples were air dried and resuspended in 50 \u00b5l nuclease free water. 5 \u00b5g of RNA was DNase treated with the TURBO DNA free Kit Ambion  AM1907 as per the manufacturer\u2019s protocol  in a volume of 50 \u00b5l for 30 min at 37\u00b0C. Instead of adding the DNase Inactivation Reagent  the reaction was cleaned up using RNAClean XP SPRI paramagnetic beads Beckman Coulter  A63987 following the manufacturer\u2019s instructions. The final elution volume was 28 \u00b5l. 1 \u00b5g DNase treated RNA samples were spiked with ERCC ExFold RNA Spike In Mixes Thermo Fisher Scientific  4456739 as per the manufacturer\u2019s protocol. Ribosomal RNAs were removed with the NEBNext rRNA Depletion Kit v2 NEB  E7400  followed by a clean up with RNAClean XP SPRI paramagnetic beads Beckman Coulter  A63987. Strand specific libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB E7760 and NEBNext Multiplex Oligos for Illumina NEB  E7335  all according to the manufacturer\u2019s protocols. For quality control and pooling purposes  the final libraries were run on a HS D1000 ScreenTape in the Agilent 2200 TapeStation System. The average library size was 278 bp. Libraries were sequenced on the Illumina HiSeq 4000.", "Zebrafish embryos were grown in embryo medium E3 at 28.5\u00b0C water temperature as per standard protocols.", "tissue:Whole body|genotype/variation:mon|developmental stage:22 hpf|clutch:13", "GSM4979515", "GSM4979515: mon clutch 13 at 22 hpf; Danio rerio; RNA Seq", "GSM4979515", null, "1", "post thawing the samples  each with 30 embryos per phenotype and time point in triplicate homogenized in 500 \u00b5l TRIzol Invitrogen/Thermo Fisher Scientific  15596026  samples were transferred into a pre spun 16 000 x g  30 s  room temperature 2 ml 5PRIME Phase Lock Gel Heavy tube Quantabio  2302830. post addition of 100 \u00b5l chloroform Sigma Aldrich  C2432  the tube was vigorously inverted for 15 sec  incubated at room temperature for 3 min and spun at 12 000 x g for 15 min at 4\u00b0C. The supernatant was transferred into a RNase free 1.7 ml tube. 150 \u00b5l buffer saturated phenol Invitrogen/Thermo Fisher Scientific  15513039 and 150 \u00b5l chloroform were added  the samples vortexed for 15 sec  and incubated and spun as before. The supernatant was transferred into a fresh RNase free 1.7 ml tube  300 \u00b5l chloroform added  the samples were vortexed  incubated and spun as before. The supernatant was transferred into a fresh RNase free 1.7 ml tube  250 \u00b5l 2 propanol VWR  BDH1133 added  the samples were inverted 10 times  samples were spun at 17 000 x g for 10 min at 4\u00b0C  and the supernatant was pipetted off. Samples were handled on ice from now on. Samples were washed three times with 1000 \u00b5l 75% ethanol in nuclease free water Invitrogen/Thermo Fisher Scientific  AM9937 followed by spinning at 17 000 x g for 5 min at 4\u00b0C. post the final wash  samples were air dried and resuspended in 50 \u00b5l nuclease free water. 5 \u00b5g of RNA was DNase treated with the TURBO DNA free Kit Ambion  AM1907 as per the manufacturer's protocol  in a volume of 50 \u00b5l for 30 min at 37\u00b0C. Instead of adding the DNase Inactivation Reagent  the reaction was cleaned up using RNAClean XP SPRI paramagnetic beads Beckman Coulter  A63987 following the manufacturer's instructions. The final elution volume was 28 \u00b5l. 1 \u00b5g DNase treated RNA samples were spiked with ERCC ExFold RNA Spike In Mixes Thermo Fisher Scientific  4456739 as per the manufacturer's protocol. Ribosomal RNAs were removed with the NEBNext rRNA Depletion Kit v2 NEB  E7400  followed by a clean up with RNAClean XP SPRI paramagnetic beads Beckman Coulter  A63987. Strand specific libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB E7760 and NEBNext Multiplex Oligos for Illumina NEB  E7335  all according to the manufacturer's protocols. For quality control and pooling purposes  the final libraries were run on a HS D1000 ScreenTape in the Agilent 2200 TapeStation System. The average library size was 278 bp. Libraries were sequenced on the Illumina HiSeq 4000.", "GEO Accession:GSM4979515", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP298388", null, null, "MR-3_R1_001.fastq.gz MR-3_R2_001.fastq.gz", "fastq fastq", 11508228600.0, 38360762.0, "GSM4979515 r1", "0:150 1:150", "A:2482384761;C:3244003263;G:3372822897;T:2407259813;N:1757866", 150, 150, null, null, 2482384761, 3244003263, 3372822897, 2407259813, 1757866, "SRX9699902", "SRS7895931", "SRA1174486", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.9383, 0.94347, 0.22403, 0.22337, 0.75777, 0.76641, 0.70885, 0.76674, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2020-12-17", "Segmentation", "Embryo", "Trunk", "Surface Structure"], [62676, "SRR13269764", "SRX9699901", "SRS7895930", "SRP298388", "PRJNA686152", "Transcriptionally regulated energy metabolism drives early erythropoiesis mon RNA seq", "GSE163454", "Transcriptome Analysis", "Transcription and metabolism both influence cell function yet dedicated transcriptional control of metabolic pathways that regulate cell fate has rarely been defined. Through a chemical suppressor screen  we discovered that inhibition of the pyrimidine biosynthesis enzyme DHODH rescues erythroid differentiation in bloodless moonshine mutant embryos defective for the transcription elongation factor tif1?. This rescue depends on the functional link of DHODH to mitochondrial respiration. Low a ketoglutarate levels caused by tif1? loss lead to histone hypermethylation. TIF? directly controls coenzyme Q synthesis gene expression and coenzyme Q levels are reduced in moonshine mutants. A coenzyme Q analogue rescues moonshine's bloodless phenotype. These results demonstrate mitochondrial metabolism is a key output of a lineage transcription factor that drives cell fate decisions in the early blood lineage. Overall design: Heterozygous mon;drl:eGFP fish were crossed with heterozygous mon fish  ensuring transmission of only one allele of drl:EGFP and embryos sorted for green fluorescence which is markedly reduced in mon mutant embryos beginning at 21 hpf. 30 phenotypically mon and wild type embryos were harvested per replicate = clutch  each clutch from one pairwise mating for RNA seq by homogenizing in TRIzol.", "parent bioproject:PRJNA562552", "pubmed:33986176", null, "mon clutch 11 at 22 hpf", "GSM4979514", null, "source name:Whole zebrafish embryos at 22 hpf|tissue:Whole body|genotype/variation:mon|developmental stage:22 hpf|clutch:11", "mon clutch 11 at 22 hpf", "Step 1: Quality control of RNA Seq datasets was performed by FastQC and Cutadapt to remove adaptor sequences and low quality regions. Step 2: The high quality reads were aligned to Ensembl genome assembly GRCz11 using Tophat 2.0.11 without xxx splicing form calls. Step 3: Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. Step 4: FPKM values were used to normalize and quantify each transcripts; the resulting list of differential expressed genes are filtered by log2 fold change > 2 and q value < 0.05. Genome build: Ensembl GRCz11 Supplementary files format and content: 30 426592019.htseq count.out.txt: Fragments Per Kilobase of transcript per Million mapped reads FPKM files contain gene names and FPKM values.", "Whole zebrafish embryos at 22 hpf", "No treatment.", "post thawing the samples  each with 30 embryos per phenotype and time point in triplicate homogenized in 500 \u00b5l TRIzol Invitrogen/Thermo Fisher Scientific  15596026  samples were transferred into a pre spun 16 000 x g  30 s  room temperature 2 ml 5PRIME Phase Lock Gel Heavy tube Quantabio  2302830. post addition of 100 \u00b5l chloroform Sigma Aldrich  C2432  the tube was vigorously inverted for 15 sec  incubated at room temperature for 3 min and spun at 12 000 x g for 15 min at 4\u00b0C. The supernatant was transferred into a RNase free 1.7 ml tube. 150 \u00b5l buffer saturated phenol Invitrogen/Thermo Fisher Scientific  15513039 and 150 \u00b5l chloroform were added  the samples vortexed for 15 sec  and incubated and spun as before. The supernatant was transferred into a fresh RNase free 1.7 ml tube  300 \u00b5l chloroform added  the samples were vortexed  incubated and spun as before. The supernatant was transferred into a fresh RNase free 1.7 ml tube  250 \u00b5l 2 propanol VWR  BDH1133 added  the samples were inverted 10 times  samples were spun at 17 000 x g for 10 min at 4\u00b0C  and the supernatant was pipetted off. Samples were handled on ice from now on. Samples were washed three times with 1000 \u00b5l 75% ethanol in nuclease free water Invitrogen/Thermo Fisher Scientific  AM9937 followed by spinning at 17 000 x g for 5 min at 4\u00b0C. post the final wash  samples were air dried and resuspended in 50 \u00b5l nuclease free water. 5 \u00b5g of RNA was DNase treated with the TURBO DNA free Kit Ambion  AM1907 as per the manufacturer\u2019s protocol  in a volume of 50 \u00b5l for 30 min at 37\u00b0C. Instead of adding the DNase Inactivation Reagent  the reaction was cleaned up using RNAClean XP SPRI paramagnetic beads Beckman Coulter  A63987 following the manufacturer\u2019s instructions. The final elution volume was 28 \u00b5l. 1 \u00b5g DNase treated RNA samples were spiked with ERCC ExFold RNA Spike In Mixes Thermo Fisher Scientific  4456739 as per the manufacturer\u2019s protocol. Ribosomal RNAs were removed with the NEBNext rRNA Depletion Kit v2 NEB  E7400  followed by a clean up with RNAClean XP SPRI paramagnetic beads Beckman Coulter  A63987. Strand specific libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB E7760 and NEBNext Multiplex Oligos for Illumina NEB  E7335  all according to the manufacturer\u2019s protocols. For quality control and pooling purposes  the final libraries were run on a HS D1000 ScreenTape in the Agilent 2200 TapeStation System. The average library size was 278 bp. Libraries were sequenced on the Illumina HiSeq 4000.", "Zebrafish embryos were grown in embryo medium E3 at 28.5\u00b0C water temperature as per standard protocols.", "tissue:Whole body|genotype/variation:mon|developmental stage:22 hpf|clutch:11", "GSM4979514", "GSM4979514: mon clutch 11 at 22 hpf; Danio rerio; RNA Seq", "GSM4979514", null, "1", "post thawing the samples  each with 30 embryos per phenotype and time point in triplicate homogenized in 500 \u00b5l TRIzol Invitrogen/Thermo Fisher Scientific  15596026  samples were transferred into a pre spun 16 000 x g  30 s  room temperature 2 ml 5PRIME Phase Lock Gel Heavy tube Quantabio  2302830. post addition of 100 \u00b5l chloroform Sigma Aldrich  C2432  the tube was vigorously inverted for 15 sec  incubated at room temperature for 3 min and spun at 12 000 x g for 15 min at 4\u00b0C. The supernatant was transferred into a RNase free 1.7 ml tube. 150 \u00b5l buffer saturated phenol Invitrogen/Thermo Fisher Scientific  15513039 and 150 \u00b5l chloroform were added  the samples vortexed for 15 sec  and incubated and spun as before. The supernatant was transferred into a fresh RNase free 1.7 ml tube  300 \u00b5l chloroform added  the samples were vortexed  incubated and spun as before. The supernatant was transferred into a fresh RNase free 1.7 ml tube  250 \u00b5l 2 propanol VWR  BDH1133 added  the samples were inverted 10 times  samples were spun at 17 000 x g for 10 min at 4\u00b0C  and the supernatant was pipetted off. Samples were handled on ice from now on. Samples were washed three times with 1000 \u00b5l 75% ethanol in nuclease free water Invitrogen/Thermo Fisher Scientific  AM9937 followed by spinning at 17 000 x g for 5 min at 4\u00b0C. post the final wash  samples were air dried and resuspended in 50 \u00b5l nuclease free water. 5 \u00b5g of RNA was DNase treated with the TURBO DNA free Kit Ambion  AM1907 as per the manufacturer's protocol  in a volume of 50 \u00b5l for 30 min at 37\u00b0C. Instead of adding the DNase Inactivation Reagent  the reaction was cleaned up using RNAClean XP SPRI paramagnetic beads Beckman Coulter  A63987 following the manufacturer's instructions. The final elution volume was 28 \u00b5l. 1 \u00b5g DNase treated RNA samples were spiked with ERCC ExFold RNA Spike In Mixes Thermo Fisher Scientific  4456739 as per the manufacturer's protocol. Ribosomal RNAs were removed with the NEBNext rRNA Depletion Kit v2 NEB  E7400  followed by a clean up with RNAClean XP SPRI paramagnetic beads Beckman Coulter  A63987. Strand specific libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB E7760 and NEBNext Multiplex Oligos for Illumina NEB  E7335  all according to the manufacturer's protocols. For quality control and pooling purposes  the final libraries were run on a HS D1000 ScreenTape in the Agilent 2200 TapeStation System. The average library size was 278 bp. Libraries were sequenced on the Illumina HiSeq 4000.", "GEO Accession:GSM4979514", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP298388", null, null, "MR-2_R1_001.fastq.gz MR-2_R2_001.fastq.gz", "fastq fastq", 12482837100.0, 41609457.0, "GSM4979514 r1", "0:150 1:150", "A:2719354476;C:3494766828;G:3624849226;T:2641955182;N:1911388", 150, 150, null, null, 2719354476, 3494766828, 3624849226, 2641955182, 1911388, "SRX9699901", "SRS7895930", "SRA1174486", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.94131, 0.94612, 0.22642, 0.22545, 0.75026, 0.75775, 0.72882, 0.73426, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2020-12-17", "Segmentation", "Embryo", "Trunk", "Surface Structure"], [62677, "SRR13269763", "SRX9699900", "SRS7895928", "SRP298388", "PRJNA686152", "Transcriptionally regulated energy metabolism drives early erythropoiesis mon RNA seq", "GSE163454", "Transcriptome Analysis", "Transcription and metabolism both influence cell function yet dedicated transcriptional control of metabolic pathways that regulate cell fate has rarely been defined. Through a chemical suppressor screen  we discovered that inhibition of the pyrimidine biosynthesis enzyme DHODH rescues erythroid differentiation in bloodless moonshine mutant embryos defective for the transcription elongation factor tif1?. This rescue depends on the functional link of DHODH to mitochondrial respiration. Low a ketoglutarate levels caused by tif1? loss lead to histone hypermethylation. TIF? directly controls coenzyme Q synthesis gene expression and coenzyme Q levels are reduced in moonshine mutants. A coenzyme Q analogue rescues moonshine's bloodless phenotype. These results demonstrate mitochondrial metabolism is a key output of a lineage transcription factor that drives cell fate decisions in the early blood lineage. Overall design: Heterozygous mon;drl:eGFP fish were crossed with heterozygous mon fish  ensuring transmission of only one allele of drl:EGFP and embryos sorted for green fluorescence which is markedly reduced in mon mutant embryos beginning at 21 hpf. 30 phenotypically mon and wild type embryos were harvested per replicate = clutch  each clutch from one pairwise mating for RNA seq by homogenizing in TRIzol.", "parent bioproject:PRJNA562552", "pubmed:33986176", null, "mon clutch 9 at 22 hpf", "GSM4979513", null, "source name:Whole zebrafish embryos at 22 hpf|tissue:Whole body|genotype/variation:mon|developmental stage:22 hpf|clutch:9", "mon clutch 9 at 22 hpf", "Step 1: Quality control of RNA Seq datasets was performed by FastQC and Cutadapt to remove adaptor sequences and low quality regions. Step 2: The high quality reads were aligned to Ensembl genome assembly GRCz11 using Tophat 2.0.11 without xxx splicing form calls. Step 3: Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. Step 4: FPKM values were used to normalize and quantify each transcripts; the resulting list of differential expressed genes are filtered by log2 fold change > 2 and q value < 0.05. Genome build: Ensembl GRCz11 Supplementary files format and content: 30 426592019.htseq count.out.txt: Fragments Per Kilobase of transcript per Million mapped reads FPKM files contain gene names and FPKM values.", "Whole zebrafish embryos at 22 hpf", "No treatment.", "post thawing the samples  each with 30 embryos per phenotype and time point in triplicate homogenized in 500 \u00b5l TRIzol Invitrogen/Thermo Fisher Scientific  15596026  samples were transferred into a pre spun 16 000 x g  30 s  room temperature 2 ml 5PRIME Phase Lock Gel Heavy tube Quantabio  2302830. post addition of 100 \u00b5l chloroform Sigma Aldrich  C2432  the tube was vigorously inverted for 15 sec  incubated at room temperature for 3 min and spun at 12 000 x g for 15 min at 4\u00b0C. The supernatant was transferred into a RNase free 1.7 ml tube. 150 \u00b5l buffer saturated phenol Invitrogen/Thermo Fisher Scientific  15513039 and 150 \u00b5l chloroform were added  the samples vortexed for 15 sec  and incubated and spun as before. The supernatant was transferred into a fresh RNase free 1.7 ml tube  300 \u00b5l chloroform added  the samples were vortexed  incubated and spun as before. The supernatant was transferred into a fresh RNase free 1.7 ml tube  250 \u00b5l 2 propanol VWR  BDH1133 added  the samples were inverted 10 times  samples were spun at 17 000 x g for 10 min at 4\u00b0C  and the supernatant was pipetted off. Samples were handled on ice from now on. Samples were washed three times with 1000 \u00b5l 75% ethanol in nuclease free water Invitrogen/Thermo Fisher Scientific  AM9937 followed by spinning at 17 000 x g for 5 min at 4\u00b0C. post the final wash  samples were air dried and resuspended in 50 \u00b5l nuclease free water. 5 \u00b5g of RNA was DNase treated with the TURBO DNA free Kit Ambion  AM1907 as per the manufacturer\u2019s protocol  in a volume of 50 \u00b5l for 30 min at 37\u00b0C. Instead of adding the DNase Inactivation Reagent  the reaction was cleaned up using RNAClean XP SPRI paramagnetic beads Beckman Coulter  A63987 following the manufacturer\u2019s instructions. The final elution volume was 28 \u00b5l. 1 \u00b5g DNase treated RNA samples were spiked with ERCC ExFold RNA Spike In Mixes Thermo Fisher Scientific  4456739 as per the manufacturer\u2019s protocol. Ribosomal RNAs were removed with the NEBNext rRNA Depletion Kit v2 NEB  E7400  followed by a clean up with RNAClean XP SPRI paramagnetic beads Beckman Coulter  A63987. Strand specific libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB E7760 and NEBNext Multiplex Oligos for Illumina NEB  E7335  all according to the manufacturer\u2019s protocols. For quality control and pooling purposes  the final libraries were run on a HS D1000 ScreenTape in the Agilent 2200 TapeStation System. The average library size was 278 bp. Libraries were sequenced on the Illumina HiSeq 4000.", "Zebrafish embryos were grown in embryo medium E3 at 28.5\u00b0C water temperature as per standard protocols.", "tissue:Whole body|genotype/variation:mon|developmental stage:22 hpf|clutch:9", "GSM4979513", "GSM4979513: mon clutch 9 at 22 hpf; Danio rerio; RNA Seq", "GSM4979513", null, "1", "post thawing the samples  each with 30 embryos per phenotype and time point in triplicate homogenized in 500 \u00b5l TRIzol Invitrogen/Thermo Fisher Scientific  15596026  samples were transferred into a pre spun 16 000 x g  30 s  room temperature 2 ml 5PRIME Phase Lock Gel Heavy tube Quantabio  2302830. post addition of 100 \u00b5l chloroform Sigma Aldrich  C2432  the tube was vigorously inverted for 15 sec  incubated at room temperature for 3 min and spun at 12 000 x g for 15 min at 4\u00b0C. The supernatant was transferred into a RNase free 1.7 ml tube. 150 \u00b5l buffer saturated phenol Invitrogen/Thermo Fisher Scientific  15513039 and 150 \u00b5l chloroform were added  the samples vortexed for 15 sec  and incubated and spun as before. The supernatant was transferred into a fresh RNase free 1.7 ml tube  300 \u00b5l chloroform added  the samples were vortexed  incubated and spun as before. The supernatant was transferred into a fresh RNase free 1.7 ml tube  250 \u00b5l 2 propanol VWR  BDH1133 added  the samples were inverted 10 times  samples were spun at 17 000 x g for 10 min at 4\u00b0C  and the supernatant was pipetted off. Samples were handled on ice from now on. Samples were washed three times with 1000 \u00b5l 75% ethanol in nuclease free water Invitrogen/Thermo Fisher Scientific  AM9937 followed by spinning at 17 000 x g for 5 min at 4\u00b0C. post the final wash  samples were air dried and resuspended in 50 \u00b5l nuclease free water. 5 \u00b5g of RNA was DNase treated with the TURBO DNA free Kit Ambion  AM1907 as per the manufacturer's protocol  in a volume of 50 \u00b5l for 30 min at 37\u00b0C. Instead of adding the DNase Inactivation Reagent  the reaction was cleaned up using RNAClean XP SPRI paramagnetic beads Beckman Coulter  A63987 following the manufacturer's instructions. The final elution volume was 28 \u00b5l. 1 \u00b5g DNase treated RNA samples were spiked with ERCC ExFold RNA Spike In Mixes Thermo Fisher Scientific  4456739 as per the manufacturer's protocol. Ribosomal RNAs were removed with the NEBNext rRNA Depletion Kit v2 NEB  E7400  followed by a clean up with RNAClean XP SPRI paramagnetic beads Beckman Coulter  A63987. Strand specific libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina NEB E7760 and NEBNext Multiplex Oligos for Illumina NEB  E7335  all according to the manufacturer's protocols. For quality control and pooling purposes  the final libraries were run on a HS D1000 ScreenTape in the Agilent 2200 TapeStation System. The average library size was 278 bp. Libraries were sequenced on the Illumina HiSeq 4000.", "GEO Accession:GSM4979513", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP298388", null, null, "MR-1_R1_001.fastq.gz MR-1_R2_001.fastq.gz", "fastq fastq", 12056308200.0, 40187694.0, "GSM4979513 r1", "0:150 1:150", "A:2635931132;C:3374069335;G:3499037426;T:2545435782;N:1834525", 150, 150, null, null, 2635931132, 3374069335, 3499037426, 2545435782, 1834525, "SRX9699900", "SRS7895928", "SRA1174486", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.93773, 0.9425, 0.22425, 0.22339, 0.7545, 0.76242, 0.7295, 0.74041, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2020-12-17", "Segmentation", "Embryo", "Trunk", "Surface Structure"]], "truncated": false, "filtered_table_rows_count": 7, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"devstage_curation\" = :p0 and \"tissue_curation\" = :p1 order by rowid limit 101", "params": {"p0": "Segmentation", "p1": "Trunk"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Segmentation&tissue_curation=Trunk", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 7, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Segmentation&tissue_curation=Trunk&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": 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"http://metadata.rnaquarium.org/metadata/run_metadata.json?tissue_curation=Trunk", "selected": true}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Segmentation&tissue_curation=Trunk", "results": [{"value": "Surface Structure", "label": "Surface Structure", "count": 7, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Segmentation&tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Segmentation&tissue_curation=Trunk", "results": [{"value": "Trunk", "label": "Trunk", "count": 7, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Segmentation", "selected": true}], "truncated": 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