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Sample GSM2027307 Query DataSets for GSM2027307
Status Public on Feb 17, 2016
Title RNAseq_IMR-32_Y3mut-infected_1
Sample type SRA
 
Source name IMR-32 neuroblastoma cells
Organism Homo sapiens
Characteristics cell line: IMR-32
cell type: neuroblastoma cells
lentiviral infection: infected with Y3 mut RNA
Treatment protocol For UV treatment, cells were washed in PBS exposed to 0.5 mJ/cm2 UVC and allowed to recover for 24h before being harvested
RNAi protocol: Cells were treated with mock or nELAVL RNAi for 96 hours before being harvested
Lentiviral infection protocol: Cells were infected with lentivirus 72 hours before being harvested
Growth protocol IMR-32 neuroblastoma cells were grown under standard conditions.
Extracted molecule total RNA
Extraction protocol Trizol extraction
Illumina High-throughput TruSeq RNA Sample preparation: ribominus selection (Invitrogen)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description overexpression of Y3 mut RNA
Data processing alignment with Tophat (unambigous mapping; mean inner distance: 20; st.dev.: 20)
inference of exon junctions (Bayesian method)
Genome_build: hg18
Supplementary_files_format_and_content: txt file containing geneID (Entrez) and symbol, raw reads and rpkm values
 
Submission date Jan 04, 2016
Last update date May 15, 2019
Contact name Claudia Scheckel
E-mail(s) claudia.scheckel@gmail.com
Organization name University Hospital Zurich
Department Institute of Neuropathology
Street address Schmelzbergstrasse 12
City Zurich
State/province NY
ZIP/Postal code 8091
Country Switzerland
 
Platform ID GPL16791
Series (2)
GSE53698 RNAseq in IMR-32 neuroblastoma cells
GSE53699 nELAVL HITS-CLIP and RNA-seq in Alzheimer's Disease patients and IMR-32 neuroblastoma cells
Relations
BioSample SAMN04383701
SRA SRX1515443

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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