RNA Extraction from 3D Cell Cultures

D2.OR cells were nonenzymatically isolated from 3D-culture using the Cultrex 3D-Culture Cell Harvesting Kit (Trevigen), and RNA was extracted using the RNeasy Mini Kit (QIAGEN). For patient-derived xenograft and tumor biopsy specimens, tissues were homogenized in TRIzol reagent (1 ml TRIzol/100 mg tissue), followed by RNA extraction and removal of DNA with DNase I treatment (Invitrogen). qRT-PCR was carried out as described (Gooding et al, 2017 (link)) using the primers listed in Table S2.

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Robinson N.J., Morrison-Smith C.D., Gooding A.J., Schiemann B.J., Jackson M.W., Taylor D.J, & Schiemann W.P. (2020). SLX4IP and telomere dynamics dictate breast cancer metastasis and therapeutic responsiveness. Life Science Alliance, 3(4), e201900427.

Publication 2020

Cultrex 3D-Culture Cell Harvesting Kit RNeasy Mini Kit DNase I treatment

Biopsy Cells Culture cell Dnase i Patient Primers Tissue Trizol Tumor Xenograft

Corresponding Organization : Case Western Reserve University

Other organizations : University School

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Variable analysis

independent variables

Cultrex 3D-Culture Cell Harvesting Kit (Trevigen)

dependent variables

Gene expression measured by qRT-PCR

control variables

Cell type (D2.OR cells)
RNA extraction method (RNeasy Mini Kit, QIAGEN)
RNA extraction from patient-derived xenograft and tumor biopsy specimens (TRIzol reagent, DNA removal by DNase I treatment)

controls

Positive control: Not specified
Negative control: Not specified

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