2015-04-17

The raw sequencing reads were filtered for adapter and low quality sequences using cutadapt (Martin, 2011) and custom scripts. Low quality reads were defined as sequencing reads with more than 5% unknown bases (a~Na) and reads with more than 50% of the bases having a base quality value of a 10. Reads with length < 40bp were further discarded. Finally, sequencing reads were filtered for rRNA sequence and remaining high quality reads were used for downstream analysis.The high-quality reads were aligned against human genome assembly (NCBI Build 37.1/hg19) using TopHat v2.0.8b (Kim et al, 2013). Expression estimation and tests for differential expression were processed by Cufflinks v2.1.1 (Trapnell et al, 2013). All data was expressed as Fragments Per Kilobase of exon per Million fragments mapped (FPKM) values and fold changes in transcript levels relative to the Bel-7402 shCtl group.Genome_build: hg19

Lin, CH, Lau, YT, Lee, KW. (2015). GSM1660910: 41_P1-3. [Data File]. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1660910

Homo sapiens