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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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CUT&RUN sequencing of human kidney tubuloid to study genome-wide binding site in tRCC patients

ABSTRACT: Translocation renal cell carcinoma (tRCC) is a rare, aggressive kidney cancer primarily occurring in children. They are genetically defined by translocations involving MiT/TFE gene family members, TFE3. We utilized human kidney organoids, or tubuloids, to engineer a tRCC model by expressing of one of the most common MiT/TFE fusions, SFPQ-TFE3. Lentiviral transductions were performed as previously described with lentiviruses encoding either pLKO.1-UbC-luciferase-blast (TubCtrl), pLKO.1-UbC-TFE3-blast (TubTFE3), or pLKO.1-UbC-SFPQ-TFE3-blast (TubFus). Two days post transduction, 5 µg/ml blasticidin was added to the culture medium to select for successfully transduced cells. To study the genome-wide binding sites of the fusion, we conducted CUT&RUN sequencing. CUT&RUN experiments were performed using a modified protocol for low cell numbers using the following antibodies: anti-TFE3 (ab93808, Abcam, 1:2000). Libraries were sequenced using an Illumina NextSeq2000 (2x100bp).

INSTRUMENT(S): Illumina NextSeq2000 (2x100bp), NextSeq 2000

ORGANISM(S): Homo sapiens

SUBMITTER: Nhung Pham

PROVIDER: E-MTAB-13900 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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