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Sample GSM1216745 Query DataSets for GSM1216745
Status Public on Nov 26, 2013
Title RNA_DL23_4OHT_8h_Rep1
Sample type SRA
 
Source name DL23 cell line with pcDNA3-HA-FOXO33-ER
Organism Homo sapiens
Characteristics cell line: DL23 cell line with pcDNA3-HA-FOXO33-ER
Growth protocol DLD1 and DLD1-F3 cells were grown on RPMI-1640 medium with 10% FCS and standard supplements
Extracted molecule polyA RNA
Extraction protocol Sequencing libraries were constructed using SOLiD® Total RNA-Seq Kit (Life technologies) according to the standard protocol recommendations for low input and sequenced on SOLiD sequencer in a multiplexed way to produce 50-bp long reads.
To isolate polyadenylated and capped RNA, total RNA was purified using Poly(A)Purist MAG Kit (Life Technologies) according to manufacturer's instructions. Isolated RNA was subsequently re-purified using mRNA-ONLY Eukaryotic mRNA Isolation Kit (Epicentre).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model AB 5500xl Genetic Analyzer
 
Data processing Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using the BWA package (Li and Durbin, 2009). Non-uniquely placed reads were discarded.
Cisgenome v2.0 software package was used to calculate reads per 1000 base pairs of transcript per million reads sequenced (RPKM) values for all RefSeq annotated genes.
Genome_build: hg19
Supplementary_files_format_and_content: alignment file (chr;start;end;strand)
 
Submission date Aug 27, 2013
Last update date May 15, 2019
Contact name Michal Mokry
E-mail(s) m.mokry@umcutrecht.nl
Organization name Wilhelmina Children's Hospital, University Medical Center Utrecht
Street address Lundlaan 6
City Utrecht
ZIP/Postal code 3584 EA
Country Netherlands
 
Platform ID GPL16288
Series (1)
GSE50243 FOXO3 selectively amplifies enhancer activity to establish target gene regulation.
Relations
BioSample SAMN02335200
SRA SRX340066

Supplementary file Size Download File type/resource
GSM1216745_RNADL234OHT8hRep1.RPKM.gz 698.2 Kb (ftp)(http) RPKM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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