Pipeline publication

[…] rified using G25 columns (GE Healthcare Life Sciences) then they were hybridized separately with the corresponding membrane at 42 °C overnight. The membrane was washed twice at room temperature with low stringent buffer (2 × SSC and 0.1% SDS) for 10 min each followed by two washes of warm high stringency buffer (0.1 × SSC and 0.1% SDS) at 55 °C for 15 min each. The membranes were left for exposure overnight and scanned with Fuji FLA7000 phosphoimager., The hg19 (GRCh37) genome version for alignment and transcript annotation from GENCODE version 19 (equivalent Ensembl GRCh37)57 was used for processing RNA-sequencing samples. Color space reads from SOLID sequencing platform were aligned using LifeScope, and HISAT58 aligner was used for reads from Illumina sequencing platform. The reads for gencode transcripts were quantified using HTSeq-count59 with ‘intersection-strict’ mode., For each S-phase time point, RNA from two independent experiments were pooled into one sample and deep sequenced on SOLID sequencing platform at Uppsala Genome Center. The alignment resulted in 18.5, 39.3, 21.3, and 29 million mappable 75 bp reads for unsynchronized, S-phase T1, S-phase T2, and S-phase T3 EtU-labeled samples, respectively. For unlabeled samples, we obtained 19.6, 30, 29, and 27 million mappable 75 bp reads for unsynchronized, S-phase T1, S-phase T2, and S-phase T3 samples, respectively., The uniquely mapped reads were assigned to long noncoding transcripts from Gencode v19 annotation and obtained 4039 and 3966 lncRNAs from EtU labeled and […]

Pipeline specifications

Software tools LifeScope, HISAT, HTSeq
Organisms Homo sapiens, Homo sapiens/Mus musculus xenograft
Diseases Neoplasms