run_metadata: 36500
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 36500 | SRR535852 | SRX174969 | SRS353001 | SRP014772 | PRJNA172016 | Danio rerio strain:*AB Variation | PRJNA172016 | Other | Forward genetic screens have elucidated molecular pathways required for innumerable aspects of life however identifying the causal mutations from such screens has long been the bottleneck in the process particularly in vertebrates. We have developed an RNA Seq based approach that identifies both the region of the genome linked to a mutation and candidate lesions that may be causal for the phenotype of interest. We show that our method successfully identifies zebrafish mutations that cause nonsense or missense changes to codons alter transcript splicing or alter gene expression levels. Furthermore we develop an online accessible or downloadable bioinformatics pipeline allowing for easy implementation of all steps of the method. Overall we show that RNA Seq is a fast reliable and cost effective method to map and identify mutations that will greatly facilitate the power of forward genetics in vertebrate models. | RNA seq data from Miller et al submitted. Data was generated in order to map ENU induced mutations in zebrafish. This data hox80 was created from 80 pooled hoxb1bb1219 fish that were the siblings of wt80. | Miller hox80.bam | Miller hox80.bam | Miller hox80.bam | Miller hox80.bam | 1 | 1 | RNA-Seq | TRANSCRIPTOMIC | RT-PCR | PAIRED | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | SRP014772 | hox80.bam | bam | 1678151069.0 | 18115874.0 | Miller hox80.bam | 0:49 1:49 | A:431345472;C:411044967;G:399581415;T:436154722;N:24493 | 49 | 49 | 431345472 | 411044967 | 399581415 | 436154722 | 24493 | SRX174969 | SRS353001 | SRA056859 | Fred Hutchinson Cancer Research Center|Moens | Fred Hutchinson Cancer Research Center | 2 | 0.9641 | 0.96398 | 0.06923 | 0.06967 | 0.67292 | 0.67351 | 0.47172 | 0.46487 | 49 | 49 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | other | unknown | bulk | unknown | unknown | United States | 2012-11-30 | Undetermined | Undetermined | Undetermined | Undetermined |