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| Status |
Public on Mar 27, 2018 |
| Title |
THP1_DMSO_replicate2 |
| Sample type |
SRA |
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| Source name |
THP1 cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: acute myeloid leukemia (AML)
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| Treatment protocol |
THP1 AML cells were treated with 250nM OG86 or DMSO vehicle for 24 hours in semi-solid culture.
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| Growth protocol |
THP1 cells were cultured in methylcellulose (H4320, Stem Cell Technologies, Vancouver, BC) without supplemental growth factors.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from vehicle or OG86-treated THP1 AML cells using QIAshredder spin columns and an RNeasy Plus Micro Kit (Qiagen, Manchester, UK).
PolyA selection using 15µg total RNA was carried out by performing three rounds of selection using a MicroPoly(A)Purist Kit. Barcoded polyA libraries for pooling and sequencing were prepared using 55ng of the polyA selected RNA with a SOLiD Total RNA-seq Kit. Following quantitation of the libraries by Q-PCR using a SOLiD Library TaqMan Quantitation Kit, emulsion PCR was performed using the SOLiD EZBead System prior to sequencing of single-ended strand-specific 50mers using a SOLiD 5500 System (all from Life Technologies, Paisley, UK).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500 Genetic Analyzer |
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| Data processing |
Reads were aligned to the human genome (build hg19) with SHRIMP2 (Langmead et al., 2009; David et al., 2011) using default settings. Reads aligning to multiple loci were discarded. There were 58.5 million and 67.6 million uniquely mapped reads for the DMSO and OG86 treated THP1 cell samples respectively. Data from two technical replicates for each sample were merged. 90.8% and 90.5% of reads mapped to annotated protein coding genes (ENSEMBL v66) using the annmap database, R and Bioconductor (Gentleman et al., 2004; Yates et al., 2007). RPKM (reads per kilobase per million uniquely mapped reads) was computed for each transcript. Gene level expression values were calculated as the mean RPKM expression for all transcripts arising from the same annotated gene. Genes annotated as protein coding in ENSEMBL v66 but not by the Human Genome Consortium (www.genenames.org, access date 31 March 2014) were discarded, as were mitochondrial genes, leaving 18670 for analysis. Once genes with expression levels less than 2 RPKM in both samples were discarded, 10,007 remained for downstream analyses (processed data file).
Genome_build: hg19
Supplementary_files_format_and_content: Processed data file. Gene expression in THP1 AML cells treated with 250nM OG86 or DMSO vehicle. Only expressed genes were considered in the analysis (i.e. the 10,007 Human Genome Consortium annotated protein-coding genes exhibiting expression levels of >2.0 reads per kilobase per million mapped reads (RPKM) in at least one of the samples ).
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| Submission date |
Nov 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Tim C Somervaille |
| E-mail(s) |
tim.somervaille@cruk.manchester.ac.uk
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| Organization name |
Cancer Research UK Manchester Institute
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| Lab |
Leukaemia Biology Laboratory
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| Street address |
Wilmslow Road
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| City |
Manchester |
| State/province |
Lancashire |
| ZIP/Postal code |
M20 4BX |
| Country |
United Kingdom |
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| Platform ID |
GPL16558 |
| Series (2) |
| GSE63217 |
Inhibitors of LSD1 target demethylase-independent activity to induce differentiation in acute myeloid leukemia [RNA-Seq experiments] |
| GSE63222 |
Inhibitors of LSD1 target demethylase-independent activity to induce differentiation in acute myeloid leukemia |
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| Relations |
| BioSample |
SAMN03177314 |
| SRA |
SRX758157 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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