GSM3693064: High ARID3A and Low ARID3B 1; Homo sapiens; RNA-Seq
RNA was collected using RNAeasy kit (Qiagen) according to manufacturer's instructions. RNA-seq libraries were prepared at the University of Notre Dame Genomics and Bioinformatics Core Facility. Total RNA samples were diluted 5 times prior to analysis.  Sample concentration was measured using Qubit RNA HS Assay Kit (PN: Q32855; Invitrogen, Carlsbad, CA, USA). Total RNA evaluate with Agilent Bioanlayzer 2100 System and Agilent RNA 6000 Nano Kit (PN: 5067-1511; Agilent Technologies, Santa Clara, CA, USA). Samples with an RNA Integrity Number (RIN) of 7 or higher were qualified for library preparation. Sample 2 and Sample 4 with RIN of 6.9 were included in the study. Total RNA input was normalized to 150 ng. Polyadendylated RNA molecules were selected for using NEBNext Poly(A) mRNA Magnetic Isolation Module (PN: E7490S/L; New England BioLabs, Ipswich, MA, USA).  Enriched polyadendylated RNA was converted into an Illumina library using NEBNext Ultra II RNA Library Prep with Sample Purification Beads (PN: E7775S/L; New England BioLabs, Ipswich, MA, USA) and barcoded with NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) (PN: E7335S/L; New England BioLabs, Ipswich, MA, USA) or NEBNext Multiplex Oligos for Illumina (Index Primers Set 2) (PN: E7500S/L; New England BioLabs, Ipswich, MA, USA). Indexed libraries were quantitated with Qubit dsDNA HS Assay Kit (PN: Q32854; Invitrogen, Carlsbad, CA, USA). Library quality assessment with Agilent DNA 7500 Kit (PN: 5067-1506; Agilent Technologies, Santa Clara, CA, USA). The individual libraries were normalized, and equal molar amounts were multiplexed into a single pool.  Molar concentration of the multiplex pool was determined with KAPA Library Quantification Kits for Illumina (PN: KK4824; KAPA Biosystems, Boston, MA, USA). Materials used: NEBNext Ultra II RNA Library Prep with Sample Purification Beads (PN: E7775S/L; New England BioLabs, Ipswich, MA, USA), NEBNext Poly(A) mRNA Magnetic Isolation Module (PN: E7490S/L; New England BioLabs, Ipswich, MA, USA), NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) (PN: E7335S/L; New England BioLabs, Ipswich, MA, USA), NEBNext Multiplex Oligos for Illumina (Index Primers Set 2) (PN: E7500S/L; New England BioLabs, Ipswich, MA, USA), Agilent RNA 6000 Nano Kit (PN: 5067-1511; Agilent Technologies, Santa Clara, CA, USA). Agilent DNA 7500 Kit (PN: 5067-1506; Agilent Technologies, Santa Clara, CA, USA), Qubit RNA HS Assay Kit (PN: Q32855; Invitrogen, Carlsbad, CA, USA), Qubit dsDNA HS Assay Kit (PN: Q32854; Invitrogen, Carlsbad, CA, USA), and KAPA Library Quantification Kits for Illumina (PN: KK4824; KAPA Biosystems, Boston, MA, USA).
GEO Accession
GSM3693064