run_metadata: 24550
This data as json
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| 24550 | ERR964668 | ERX1041631 | ERS792102 | ERP011038 | PRJEB9889 | The Zebrafish transcriptome during early development | ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22 | Other | Zebrafish has emerged as a model organism to investigate vertebrate development and human genetic diseases. However currently zebrafish annotation is still ongoing and clearly not sufficed therefore providing opportunity for novel transcript finding. With the introduction of massive parallel sequencing whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation. | KI BN JKE DRERIO RNASEQ | SAMEA3484817 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484817|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 16cell|common name:zebrafish|dev stage:16 cell|sample name:KI BN JKE DRERIO RNASEQ 2009 16cell|strain:Tuebingen | AB SOLiD System 3.0 sequencing | ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:870 2 | unspecified | 1 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | ERP011038 | AB SOLiD System 3.0 sequencing | ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16 | KI-BN-JKE-DRERIO-RNASEQ-20090709-16cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20090709-16cell_F3_QV.qual.gz | SOLiD_native SOLiD_native | 5278508300.0 | 105570166.0 | ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:871 2 | 0:50 | 0:1410981717;1:1203936808;2:1415708111;3:1223403795;.:24477869 | 50 | ERX1041631 | ERS792102 | ERA458495 | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive | KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION | 1 | 0.71371 | 0.09346 | 0.91539 | 0.73015 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | unknown | bulk | unknown | unknown | Sweden | 2015-07-15 | Cleavage | Embryo | Undetermined | Embryo Imprecise |