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Series GSE75452 Query DataSets for GSE75452
Status Public on Oct 25, 2016
Title Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary To identify genes regulated by NFE2L2 (Nrf2), we selected a lung cancer cell line (A549) in which NFE2L2 is normally active. Three transfections using siRNAs targeting NFE2L2 and four control transfections using two different negative control siRNAs were done. As a result, we found several genes up or down regulated in response to NFE2L2 inactivation in these cells.
Overall design A549 cells were cultured, and 250,000 cells were transfected with Lipofectamine RNAiMAX reagent containing 5 nmol siRNA particles in a 6-well plate. Three transfections with siRNAs targeting NFE2L2 were performed, using three independent duplexes, while four control transfections were done using two different control duplexes, in addition to one mock (Lipofectamine only) transfection. RNA was prepared using the RNeasy Mini kit. 8 strand-specific total RNA-seq libraries were generated on an Illumina NextSeq 500. Between 50.5 and 60.6 million reads were obtained per sample. Reads were aligned to hg19 genome, at an alignment rate exceeding 94.4% for all samples.
Contributor(s) Ashouri A, Sayin VI, Van den Eynden J, Singh SX, Papagiannakopoulos T, Larsson E
Citation Ashouri, A. et al. Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events. Nat. Commun. 7, 13197
BioProject PRJNA299393
Submission date Nov 27, 2015
Last update date May 15, 2019
Contact name Arghavan Ashouri
Organization name University of Gothenburg
Department Medical Biochemistry and Cell Biology
Street address Medicinaregatan 9A
City Gothenburg
ZIP/Postal code 41390
Country Sweden
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (8)
GSM1955398 A549 - Mock transfection control
GSM1955399 A549 - NFE2L2-siRNA-1
GSM1955400 A549 - NFE2L2-siRNA-2
SRA SRP066737

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE75452_RAW.tar 1.8 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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