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Widespread chromatin activation underlies pathogenic mechanisms in multiple myeloma

ABSTRACT: RNA-seq analysis comparing the transcriptional landscape of PRDM5 silenced vs mock KMS-11 multiple myeloma cell line

ORGANISM(S): Homo sapiens

PROVIDER: GSE122638 | GEO | 2019/11/16

REPOSITORIES: GEO

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Widespread chromatin activation underlies pathogenic mechanisms in multiple myeloma

Project description:Widespread chromatin activation underlies pathogenic mechanisms in multiple myeloma

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Project description:We used a total of 10 human multiple myeloma cell lines for the study (KMS-20, KMS-28BM, MOLP-8, RPMI-8226, U-266, KMS-11, KMS-12-PE, KMS-34, LP-1 and NCI-H929). Cells (2 x 105 per well) were seeded into six-well culture plates in the appropriate culture media 24 h before treatment. Five replicate wells were then exposed to 2 uM of E7438 or control DMSO for 3 days. Cells were collected and RNA was extracted using RNeasy kit (Qiagen) according to the manufacturer’s instructions. For each sample, 250ng of total RNA was amplified using the Affymetrix GeneChip WT PLUS Reagent Kit according to the protocol described in User Manual Target Preparation for GeneChip Whole Transcript (WT) Expression Arrays (P/N 703174 Rev. 2). An Affymetrix Human Gene 2.1 ST 96-array plate was hybridized with 3µg of fragmented and labeled ss cDNA, washed, stained, and scanned according to the protocol described in User Manual GeneTitan®Instrument User Guide for Expression Arrays Plates (P/N 702933 Rev.1) and Affymetrix® GeneChip® Command Console™ User’s Guide (P/N 702569 Rev.9) using the Affymetrix GeneTitan instrument.

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