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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
10160 ERR5236191 ERX5039558 ERS5672242 ERP126773 PRJEB42852 RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf E-MTAB-10068 Transcriptome Analysis Currently there is little knowledge on the functions and signaling pathways of MAB21L1. Therefore we developed a zebrafish genetic model of mab21l1 deficiency to use in order to gain insight into possibly affected pathways and transcripts. We conducted RNA seq on zebrafish whole eyes which were dissected out at 5 dpf Three biological replicates per genotype wild type or homozygous mab21l1 c.107delA were collected with 50 eyes per replicate. RNA was extracted and purified and submitted to Macrogen to conduct RNA Sequencing procedure. ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26   Protocols: Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E. Zebrafish mab21l1 1 SAMEA7984960 Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA ENA first public:2022 01 26|ENA last update:2022 01 26|External Id:SAMEA7984960|INSDC center alias:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA|INSDC center name:Department of Pediatrics and Cell Biology Neurobiology and Anatomy The Medical College of Wisconsin Milwaukee WI USA|INSDC first public:2022 01 26T00:16:15Z|INSDC last update:2022 01 26T00:16:15Z|INSDC status:public|Submitter Id:E MTAB 10068:Zebrafish mab21l1 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:late embryonic stage|genotype:homozygous mab21l1 c.107delA|organism part:eye|sample name:E MTAB 10068:Zebrafish mab21l1 1                 Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf E MTAB 10068:Zebrafish mab21l1 1 p Zebrafish mab21l1 1 p RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf Whole eyes were dissected from 5 dpf wild type or homozygous mab21l1 c.107delA embryos into 1X Ringer's solution. Three biological samples were collected per genotype and each sample contained 50 eyes. To isolate RNA whole eye samples were lysed and homogenized in TRI Reagent. Then the Direct zol RNA MiniPrep Kit from ZymoResearch was followed to extract and purify RNA. RNA Samples were submitted to Macrogen for RNA Seq performance. Macrogen conducted library prep using a TruSeq Stranded mRNA LT Sample Prep Kit following the TruSeq Stranded mRNA Sample Preparation Guide Part # 15031047 Rev. E. Experimental Factor: genotype:homozygous mab21l1 c.107delA RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP126773 Illumina NovaSeq 6000 paired end sequencing; RNA Seq of zebrafish whole eye comparing wild type and mab21l1 c.107delA p.Lys36Argfs*7 embryos at 5 dpf ENA FIRST PUBLIC:2022 01 26|ENA LAST UPDATE:2022 01 26 Zebrafish_mab21l1_1_1.fastq.gz Zebrafish_mab21l1_1_2.fastq.gz fastq fastq 6882371922.0 22789311.0 E MTAB 10068:Zebrafish mab21l1 1 0:151 1:151 A:1803380739;C:1630414039;G:1732263332;T:1716255495;N:58317 151 151     1803380739 1630414039 1732263332 1716255495 58317 ERX5039558 ERS5672242 ERA3400155 Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive Department of Pediatrics and Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, WI USA|European Nucleotide Archive 2 0.95518 0.95612 0.07088 0.07032 0.70526 0.70457 0.42942 0.4302 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United States 2022-01-26 Larval Larval Eye Sensory System