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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
9994 ERR4568378 ERX4504051 ERS5050794 ERP123840 PRJEB40227 RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E-MTAB-9528 Other The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal middle and distal adult fin tissue of hypothyroid zebrafish with euthyroid sibling fish as control. ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12   Protocols: Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit HypoTH Distal Rep3 SAMEA7292224 BOSTON COLLEGE ENA FIRST PUBLIC:2021 04 11T00:31:24Z|ENA LAST UPDATE:2020 09 04T16:33:06Z|External Id:SAMEA7292224|INSDC center name:BOSTON COLLEGE|INSDC first public:2021 04 11T00:31:24Z|INSDC last update:2020 09 04T16:33:06Z|INSDC status:public|Submitter Id:E MTAB 9528:HypoTH Distal Rep3|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|organism part:caudal fin|phenotype:hypothyroid fish|sample name:E MTAB 9528:HypoTH Distal Rep3|sampling site:distal portion|scientific name:Danio rerio|strain:Tgtg:nVenus 2a nfnB                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH E MTAB 9528:HypoTH Distal Rep3 p HypoTH Distal Rep3 p RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH Intact caudal fin tissue was sampled from sibling adults >18 SL reared under euthyroid or hypothyroid conditions. Each fish was first anesthetized with tricaine MS 222 0.02% w/v in system water and the entire caudal fin was amputated using a razor blade. Proximal middle and distal regions of the fin were sampled immediately post and flash frozen in a dry ice ethanol bath. Three biological replicates each containing five fin regions were collected for both TH backgrounds. RNA was extracted the same day with Zymo Quick RNA Microprep kit R1050 Zymo Research Irvine CA USA. Sample libraries were made with NEBNext Ultra II RNA Library Prep kit Experimental Factor: phenotype:hypothyroid fish|Experimental Factor: sampling site:distal portion RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina NovaSeq 6000   ERP123840 Illumina NovaSeq 6000 paired end sequencing; RNA seq of proximal middle and distal caudal fin tissue of thyroid ablated zebrafish hypothyroid HypoTH and wild type zebrafish euthyroid EuTH ENA FIRST PUBLIC:2022 04 12|ENA LAST UPDATE:2022 04 12 HD3_CRRA200004865-1a_HV532DSXX_L4_1.fq.gz HD3_CRRA200004865-1a_HV532DSXX_L4_2.fq.gz fastq fastq 8040672900.0 26802243.0 E MTAB 9528:HD3 CRRA200004865 1a HV532DSXX L4 0:150 1:150 A:2167099154;C:1865357004;G:1864002622;T:2144021108;N:193012 150 150     2167099154 1865357004 1864002622 2144021108 193012 ERX4504051 ERS5050794 ERA2831606 Boston College|European Nucleotide Archive Boston College|European Nucleotide Archive 2 0.92854 0.92899 0.09996 0.09934 0.71902 0.71881 0.4815 0.47867 150 150 B B biological fallback assumption illumina novaseq_era unknown unknown nebnext bulk unknown unknown   United States 2020-09-04 Adult Adult Multi-tissue Multi-system