Dataset

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Title of Dataset
GSM1308997: HK1 (miRNA)
Author of Dataset
Lin, Chi Ho1
Szeto, Carol Y1
Choi, Siu C1
Yip, Timothy T1
Ngan, Roger K1
Contact
Lin, Chi Ho1
Date of Dataset Creation
2014-01-16
Description
Raw RNASeq reads were filtered for adapters and ribosomal RNA, followed by alignment to the human genome (hg19) and mouse genome (mm9) using the Tophat (Langmead et al., 2009; Trapnell et al., 2009) v2.0.3.1.Reads mapped to multiple locations were discarded using the aG option of Tophat. UCSC gene models were used for analysis with both software and downloaded from the Tophat website (http://tophat.cbcb.umd.edu/igenomes.html).CLC genomics workbench v5.5 (CLC bio, Denmark) was used for small RNA analysis. Adapters were trimmed under default parameter setting to retain only reads with lengths a 15 bp. These reads were then mapped and annotated against the miRBase (Griffiths-Jones, 2004; Griffiths-Jones et al., 2006; Griffiths-Jones et al., 2008; Kozomara and Griffiths-Jones, 2011) (release 19).Read counts of the annotated miRNA were exported from CLC genomics workbench and RPM (Reads per million base pairs) were calculated using customs scripts. Non-annotated reads were further mapped to Ribosomal RNA (rRNA), Transfer RNA (tRNA), Small nucleolar RNA (snoRNA), Messenger RNA (mRNA), Small nuclear RNA (snRNA), and genomic repeats.Isomirs werewas analyzed based on CLC results using custom scripts based on mature reference sequences from miRBase and novel EBV-miRNA from Chen et. al, 2010(Chen et al., 2010).Genome_build: Human genome (hg19)
Citation
Lin, CH, Szeto, CY, Lung, ML, Choi, SC, Yip, TT, Ngan, RK, Tsao, GS. (2014). GSM1308997: HK1 (miRNA). [Data File]. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1308997
Subject (RGC Codes)
M1 — Biological Sciences — 生物科學
  • 1128 — Genetics — 遺傳學
Subject (ANZSRC)
06 — BIOLOGICAL SCIENCES — 生物科學
  • 0604 — GENETICS — 遺傳學
    • 060405 — Gene Expression (incl. Microarray and other genome-wide approaches) — 基因表現
Keyword
Homo sapiens
Affiliations
  1. The University of Hong Kong, Centre for Genomic Sciences, 6th Floor, The Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam, Hong Kong, China