title: Illumina Genome Analyzer IIx paired end sequencing; Regulation of the ESC transcriptome by nuclear long non-coding RNAs
design: Regulation of the ESC transcriptome by nuclear long non-coding RNAs
library_construction_protocol: ESC colonies were maintained on gelatinized cell culture dishes, on a feeder layer of irradiated mouse embryonic fibroblasts in knock-out DMEM supplemented with 15 % fetal bovine serum, non-essential amino acids and 1,000 U/ml leukemia inhibiting factor. NPCs were maintained on gelatinized cell culture dishes in N2 expansion medium composed of 50:50 DMEM / F12: neurobasal medium, supplemented with 1x N2, 0.05x B-27, 50 ug /ml BSA (fraction V), 1ug / ml laminin, and 10 ng / ml each murine basic fibroblast growth factor and epidermal growth factor Total RNA was isolated using TRIzol reagent. For ASO knock-down studies, total RNA was collected using TRIzol and precipitated in the presence of 7.5 ug GlycoBlue (Ambion, Life Technologies). RNA integrity was assessed on the Agilent 2100 Bioanalyzer instrument and only RNA samples with integrity scores > 9.5 (median 10.0) were used. Stranded libraries for paired-end sequencing were prepared as described in Parkhomchuk, D., Borodina, T., Amstislavskiy, V., Banaru, M., Hallen, L., Krobitsch, S., Lehrach, H., and Soldatov, A. (2009). Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res. 37, e123.
identifiers.namespace: CSHL
identifiers.id: E-MTAB-3198:AB2.2 NPC total polyA
identifiers.namespace: Cold Spring Harbor Laboratory
identifiers.id: E-MTAB-3198:AB2.2 NPC total polyA