|
| Status |
Public on Sep 13, 2016 |
| Title |
MB002 EV Dox 8h |
| Sample type |
SRA |
| |
|
| Source name |
MB002 medulloblastoma cells, empty vector
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MB002
cell type: Medulloblastoma cell line
transduction: Empty vector
|
| Treatment protocol |
MB002 were treated with 100 ng/mL doxycycline in the regular propagation culture medium (described above) for 8 hours prior to being collected for extraction.
|
| Growth protocol |
MB002 were maintained in culture media made up of 1:1 (v/v) DMEM/F-12 (Gibco) and Neurobasal -A media (Gibco, #10888-022) supplemented with HEPES, sodium pyruvate, non-essential amino acid, L-glutamine, B27, 20 ng/mL EGF, 20 ng/mL basic-fibroblast growth factor, Heparin, and 10 ng/mL leukemia inhibitory factor.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed in Trizol (Life Technologies) and RNA was prepared using Qiagen RNeasy Mini Kit (Qiagen) according to manufacturer's recommendations.
RNA-Seq libraries were prepared for sequencing using standard Ion-Torrent protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent PGM |
| |
|
| Description |
MB002 Empty Vector treated with 100 ng/ml doxycycline in triplicates for 8h.
Processed data file: Expression_data_MB002_dox.tsv
|
| Data processing |
All RNA sequence reads were mapped against the human genome assembly GRCh37/hg19 using STAR v2.4.0 in a two-step approach previously described by Veeneman, B.A., et al. in Bioinformatics, 2016.
Unmapped reads were realigned using Bowtie2 v2.2 and default parameters.
Duplicate reads were removed with Piccard v1.127 and default parameters.
The transcriptome were assembled and the expression profile quantified with Cufflinks v2.2.1 and default parameters.
Comparison of transcriptomes and their expression levels were performed using Cuffcompare and Cuffdiff.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Expression_data_MB002_dox.tsv: A tab-delimited text file with FPKM values for each sample.
|
| |
|
| Submission date |
Jul 12, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Fredrik Johansson Swartling |
| Organization name |
Uppsala University
|
| Department |
Immunology, Genetics and Pathology
|
| Street address |
Dag Hammarskjölds väg 20
|
| City |
Uppsala |
| ZIP/Postal code |
752 37 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL17301 |
| Series (1) |
| GSE84320 |
RNA-Seq analysis of human medulloblastoma cell lines with SOX9 overexpression |
|
| Relations |
| BioSample |
SAMN05382494 |
| SRA |
SRX1939111 |
