run_metadata: 50597
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 |
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| 50597 | SRR8137052 | SRX4958003 | SRS3997978 | SRP167259 | PRJNA501894 | RNA Sequencing of sibling and TET2/3 DKO zebrafish | GSE121989 | Transcriptome Analysis | Ten eleven translocation Tet enzymes Tet1/2/3 mediate 5 methylcytosine 5mC hydroxylation which can facilitate DNA demethylation and thereby impact gene expression. Studied mostly for how mutant isoforms impact cancer the normal roles for Tet enzymes during organogenesis are largely unknown. By analyzing compound mutant zebrafish we discovered a requirement for Tet2/3 activity in embryonic heart for recruitment of epicardial progenitors associated with defects in development of the atrial ventricular canal AVC. Through a combination of methylation hydroxymethylation and transcript profiling the genes encoding the ActivinA subunit Inhbaa in endocardium and Sox9b in myocardium were implicated as demethylation targets of Tet2/3 and critical for organization of AVC localized extracellular matrix ECM facilitating migration of epicardial progenitors onto the developing heart tube. This study elucidates essential DNA epigenetic modifications that govern gene expression changes during cardiac development with striking temporal and lineage specificities highlighting complex interactions in multiple cell populations during development of the vertebrate heart. Overall design: For RNA Sequencing total RNA was isolated with the RNeasy Mini Kit Qiagen 74136 from 25hpf sibling and TET2/3 DKO zebrafish embryos n=3 each or 48hpf WT sibling and TET2/3 DKO zebrafish dissected heart n=2 each. | parent bioproject:PRJNA501891 | pubmed:30650362 | 48hpf WT heart 1 [RNA seq] | GSM3452697 | source name:48hpf WT heart|strain background:AB|tissue:zebrafish dissected heart|genotype/variation:Wild type sequence | 48hpf WT heart 1 [RNA seq] | Raw reads were aligned using STAR v2.3.0e r291 Read counting was performed using htseq count v0.6.0 Genome build: GRCz10 Supplementary files format and content: counts | 48hpf WT heart | No treatments were applied prior to RNA extraction | For 48hpf dissected heart total RNA was isolated with the RNeasy Micro Kit. Then 1 ng total RNA was used to prepare amplified double stranded cDNA using the Ovation RNA Seq System V2 Nugen. Amplified cDNA was purified using a QIAquick PCR purification kit Qiagen and 200 ng of amplified cDNA was fragmented in a final volume of 50 l using S220 Focused ultrasonicator Covaris to obtain 150 bp DNA fragment size peak incident power: 175W duty factor: 10% cycles per burst: 200 time: 280s. For 25hpf whole embryo RNA seq total RNA was isolated with the RNeasy Mini Kit. Fragmented DNA samples and whole embryo RNA samples were used to prepare libraries with the TruSeq RNA Library Prep Kit v2 Illumina Illumina TruSeq RNA Library Prep Kit v2 | Embryos were raised at 28.5°C and morphologically staged as described Kimmel et al. 1995; all procedures were carried out as approved by the WCMC IACUC. Wild type embryos were derived from crosses of the AB and TU lines. For heart RNA seq 48hpf embryonic hearts are dissected manually unders microscope. | strain background:AB|tissue:zebrafish dissected heart|genotype/variation:Wild type sequence | GSM3452697 | GSM3452697: 48hpf WT heart 1 [RNA seq]; Danio rerio; RNA Seq | GSM3452697 | 1 | For 48hpf dissected heart total RNA was isolated with the RNeasy Micro Kit. Then 1 ng total RNA was used to prepare amplified double stranded cDNA using the Ovation RNA Seq System V2 Nugen. Amplified cDNA was purified using a QIAquick PCR purification kit Qiagen and 200 ng of amplified cDNA was fragmented in a final volume of 50 l using S220 Focused ultrasonicator Covaris to obtain 150 bp DNA fragment size peak incident power: 175W duty factor: 10% cycles per burst: 200 time: 280s. For 25hpf whole embryo RNA seq total RNA was isolated with the RNeasy Mini Kit. Fragmented DNA samples and whole embryo RNA samples were used to prepare libraries with the TruSeq RNA Library Prep Kit v2 Illumina Illumina TruSeq RNA Library Prep Kit v2 | GEO Accession:GSM3452697 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP167259 | wt1.R1.fastq.gz | fastq | 814934763.0 | 15979113.0 | GSM3452697 r1 | 0:51 1:0 | A:228418186;C:163597853;G:147441639;T:275428487;N:48598 | 51 | 0 | 228418186 | 163597853 | 147441639 | 275428487 | 48598 | SRX4958003 | SRS3997978 | SRA801090 | GEO | Weill Cornell Medicine | 1 | 0.8131 | 0.24329 | 0.77733 | 0.55881 | 51 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | United States | 2018-10-30 | Multi-stage | Embryo | Heart | Cardiovascular System |