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Sample GSM1900662 Query DataSets for GSM1900662
Status Public on Oct 03, 2015
Title control total fraction replicate #1
Sample type SRA
 
Source name control total fraction replicate #1
Organism Homo sapiens
Characteristics cell line: HEK293
Growth protocol For PAP knockdown, cells were treated with siRNAs targeting PAPĪ± and PAPĪ³ for three days before harvesting. For LALA expression, doxycycline was removed from the media three days prior to harvesting. One day following siRNA transfection or doxycycline, cells were split to ~25% confluency and allowed to grow for two additional days.
Extracted molecule total RNA
Extraction protocol TruSeq Stranded mRNA preparation kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Samples were sequenced using Illumina HiSeq 2500 (paired-end 100 bp reads).
The reads were mapped, aligned and assembled using TopHat2 and Cufflinks2.2 (Kim et al. 2013; Trapnell et al. 2012).
Differential gene expression was analyzed by Cuffdiff using the iGenomes annotations and EdgeR was employed to determine differential expression of the 13,853 known and novel lncRNAs in the GENCODE annotation (Robinson et al. 2010).
DEGs were identified from the Cuffdiff output by removing those transcripts with an FPKM of <1 in the treatment sample and the remaining transcripts with p-value <0.05 and a false discovery rate (FDR) less than 5% were defined as DEGs. DEGs in the EdgeR data were defined as those with log(counts per million) >3.5 and an FDR <5%.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig for viewing in a genome browser; excel spreadsheet containing RPKM values
 
Submission date Oct 02, 2015
Last update date May 15, 2019
Contact name Stefan Bresson
E-mail(s) stefan.bresson@gmail.com
Organization name University of Edinburgh
Department Wellcome Trust Centre for Cell Biology
Lab Tollervey Lab
Street address Max Born Crescent, Swann 5.1
City Edinburgh
State/province Scotland
ZIP/Postal code EH9 3BF
Country United Kingdom
 
Platform ID GPL16791
Series (1)
GSE73678 Canonical poly(A) polymerase activity promotes the decay of a wide variety of mammalian nuclear RNAs
Relations
BioSample SAMN04127590
SRA SRX1300887

Supplementary file Size Download File type/resource
GSM1900662_control_total_replicate1.negativeStrand.normalized.bigWig 92.7 Mb (ftp)(http) BIGWIG
GSM1900662_control_total_replicate1.positiveStrand.normalized.bigWig 97.4 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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