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
52242,SRR9047069,SRX5823596,SRS4751717,SRP198207,PRJNA542583,Migrasomes provide regional cues for organ morphogenesis during zebrafish gastrulation,PRJNA542583,Other,Our study shows that migrasomes are signaling organelles which provide specific biochemical information to coordinate organ morphogenesis.,,,,stdMO PBS,stdMO PBS,,strain:Tu|isolate:primary cell|dev stage:gastrulation|sex:not determined|tissue:embryo|collection date:2016 11 13|genotype:wild type|geo loc name:China: Beijing|sample type:embryos|BioSampleModel:Model organism or animal,,,,,,,,,tspan RNA seq,uniprot,uniprot,RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,BGISEQ,BGISEQ-500,,SRP198207,,,161214_I137_FCHF7TTBBXX_L2_WHFISclfRAAARAAPEI-203_1.fq.gz,fastq,633650654.0,12931646.0,161214 I137 FCHF7TTBBXX L2 WHFISclfRAAARAAPEI 203 1.fq.gz,0:49 1:0,A:165787428;C:152969494;G:145599180;T:169168973;N:125579,49,0,,,165787428,152969494,145599180,169168973,125579,SRX5823596,SRS4751717,SRA885639,Tsinghua University|School of Life Sciences,Tsinghua University,1,0.93004,,0.09559,,0.753,,0.47488,,49,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-05-30,Gastrula,Embryo,Embryo Imprecise,All anatomical structures
57168,SRR11237928,SRX7849591,SRS6259054,SRP251591,PRJNA610302,Transcriptome analysis of wild type and maternal zygotic double mutant of nup85;nup133 zebrafish embryos during early development,GSE146394,Transcriptome Analysis,To study the function of zebrafish nuclear pores during early embryogenesis  we generated maternal zygotic double mutant of nup85;nup133 MZnup85;nup133 using CRISPR/Cas9 and report the transcriptome wide changes in comparison to wild type WT embryos. Our analysis reveals a dramatic delay of maternal mRNA degradation and zygotic genome activation in MZnup85;nup133 embryos during maternal to zygotic transition. Overall design: mRNA profile of zebrafish WT and MZnup85;nup133 embryos at 4.3 hpf or at stage with dome morphology,,,,MZ 7hpf Dome,GSM4379949,,source name:whole mount embryo|strain:AB|tissue:whole mount embryo|developmental stage:7 hpf nup85 / ;nup133 / ,MZ 7hpf Dome,BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50  then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters  q   phred64   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead  B. et al.  Nat. Methods  2012  and Li  B. & Dewey  C. N.  BMC Bioinformatics  2011. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,whole mount embryo,,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,,strain:AB|tissue:whole mount embryo|developmental stage:7 hpf nup85 / ;nup133 / ,GSM4379949,GSM4379949: MZ 7hpf Dome; Danio rerio; RNA Seq,GSM4379949,,1,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,GEO Accession:GSM4379949,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP251591,,,MZ_7h_Dome_1.fq.gz,fastq,1065702100.0,21314042.0,GSM4379949 r1,0:50 1:0,A:283324952;C:247492025;G:242059243;T:291819466;N:1006414,50,0,,,283324952,247492025,242059243,291819466,1006414,SRX7849591,SRS6259054,SRA1051151,GEO,"School of life science, Tsinghua University",1,0.9445,,0.07752,,0.72565,,0.4828,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2020-03-04,Gastrula,Embryo,Embryo Imprecise,All anatomical structures