run_metadata: 62670

This data as json

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
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		wild type/het clutch 11 at 22 hpf	GSM4979520		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 µl 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 µl 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°C. The supernatant was transferred into a RNase free 1.7 ml tube. 150 µl buffer saturated phenol Invitrogen/Thermo Fisher Scientific 15513039 and 150 µl 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 µl 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 µl 2 propanol VWR BDH1133 added the samples were inverted 10 times samples were spun at 17 000 x g for 10 min at 4°C and the supernatant was pipetted off. Samples were handled on ice from now on. Samples were washed three times with 1000 µl 75% ethanol in nuclease free water Invitrogen/Thermo Fisher Scientific AM9937 followed by spinning at 17 000 x g for 5 min at 4°C. post the final wash samples were air dried and resuspended in 50 µl nuclease free water. 5 µg of RNA was DNase treated with the TURBO DNA free Kit Ambion AM1907 as per the manufacturer’s protocol in a volume of 50 µl for 30 min at 37°C. 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 µl. 1 µg 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.	Zebrafish embryos were grown in embryo medium E3 at 28.5°C 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		1	post thawing the samples each with 30 embryos per phenotype and time point in triplicate homogenized in 500 µl 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 µl 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°C. The supernatant was transferred into a RNase free 1.7 ml tube. 150 µl buffer saturated phenol Invitrogen/Thermo Fisher Scientific 15513039 and 150 µl 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 µl 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 µl 2 propanol VWR BDH1133 added the samples were inverted 10 times samples were spun at 17 000 x g for 10 min at 4°C and the supernatant was pipetted off. Samples were handled on ice from now on. Samples were washed three times with 1000 µl 75% ethanol in nuclease free water Invitrogen/Thermo Fisher Scientific AM9937 followed by spinning at 17 000 x g for 5 min at 4°C. post the final wash samples were air dried and resuspended in 50 µl nuclease free water. 5 µg of RNA was DNase treated with the TURBO DNA free Kit Ambion AM1907 as per the manufacturer's protocol in a volume of 50 µl for 30 min at 37°C. 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 µl. 1 µg 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		SRP298388			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			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		United States	2020-12-17	Segmentation	Embryo	Trunk	Surface Structure