run_metadata: 173
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 173 | DRR075397 | DRX069311 | DRS075492 | DRP004473 | PRJDB5226 | Effects of local gut tumor on whole organismal gene expressions in zebrafish | DRP004473 | Other | How tumors affects whole organismal physiology remains largely unknown. To address this we established the novel gut tumor model in zebrafish Danio rerio. This model develops tumor at an early stage of juvenile development when zebrafish larvae are small <4mm enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver the gut/gut tumor and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor contributing to discovering novel tumor organ interactions and their mediators in zebrafish. | The remaining part of body of control fish 7dpf | Control body | SAMD00065411 | sample name:1 control body 150701 Hiseq3A l3 017|tissue type:Body | Illumina HiSeq 2500 sequencing of SAMD00065411 | DRX069311 | Control body | 1 | Agilent SureSelect Strand Specific RNA Prep Kit | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | DRP004473 | Illumina HiSeq 2500 sequencing of SAMD00065411 | 2653100352.0 | 73697232.0 | DRR075397 | 0:36 | A:656791658;C:620507513;G:625038612;T:750671135;N:91434 | 36 | 656791658 | 620507513 | 625038612 | 750671135 | 91434 | DRX069311 | DRS075492 | DRA005199 | ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International | The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International | 1 | 0.89666 | 0.15749 | 0.67048 | 0.47755 | 36 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Japan | 2018-09-19 | Larval | Larval | Trunk | Surface Structure |