|
| Status |
Public on Feb 17, 2016 |
| Title |
RNAseq_IMR-32_mock_noUV_1 |
| Sample type |
SRA |
| |
|
| Source name |
RNAseq_IMR-32_mock_noUV
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR-32
cell type: neuroblastoma cells
treated with: mock RNAi for 96hrs
sample group: non-stressed
RNAi: mock
|
| 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 |
mock noUV_1
non-stressed mock RNAi
|
| 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 |
Sep 16, 2015 |
| 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 |
SAMN04090379 |
| SRA |
SRX1250589 |
