|
Status |
Public on Oct 03, 2015 |
Title |
siPAP total fraction replicate #2 |
Sample type |
SRA |
|
|
Source name |
siPAP total fraction replicate #2
|
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 |
|
|
Description |
PAPOLA and PAPOLG depleted cells
|
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
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|
|
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 |
SAMN04127595 |
SRA |
SRX1300892 |