|
| Status |
Public on Nov 16, 2016 |
| Title |
d2_4h |
| Sample type |
SRA |
| |
|
| Source name |
BT168FO (Glioblastoma stem cells)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BT168 glioblastoma stem cells (De Bacco et al., Cancer Res. 2012) with Dox inducible FLAG-Omomyc
treatment: Dox treated
time: 4h
|
| Treatment protocol |
BT168FO cell cultures were treated with 250 ng/ml Doxycycline for different time periods (0-48 hours) before isolating RNA
|
| Growth protocol |
Glioblastoma stem cells BT168 (De Bacco et al., Cancer Res. 2012) carrying a Dox inducible FLAG-Omomyc (BT168FO) were grown as neurospheres in serum free neural stem cell medium supplemented with EGF and bFGF.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using TRIzol reagent
Libraries were prepared at the Istituto di Genomica Applicata (IGA) in Udine (http://www.appliedgenomics.org/) according to Illumina TruSeq RNA Sample Preparation Kits v2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
d2
|
| Data processing |
The RNA-Seq Pipeline Tophat v13 - available at RAP (https://bioinformatics.cineca.it/rap/) and including quality controls, adaptor trimming and masking of low quality sequences, tophat 2, bowtie, Cufflinks 2.2 - was used to obtain transcript reconstruction, alignment to reference genome (hg19), and expression. Transcript levels were calculated as FPKM (Fragments Per Kilobase of exon per Million fragments mapped).
Differential expression was computed through CuffDiif 2 (as well as by DEseq)
Genome_build: hg19
Supplementary_files_format_and_content: Matrix in tab-delimited text format, including FPKM values for each Sample
|
| |
|
| Submission date |
Sep 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Federico Zambelli |
| Organization name |
University of Milan
|
| Department |
Department of Biosciences
|
| Street address |
Via Giovanni Celoria 26
|
| City |
Milano |
| ZIP/Postal code |
20133 |
| Country |
Italy |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE86518 |
Genome-wide mRNA expression in human glioblastoma cells and glioblastoma stem cells expressing or not Omomyc |
| GSE86519 |
Resetting cancer stem cell regulatory nodes upon MYC inhibition |
|
| Relations |
| BioSample |
SAMN05736260 |
| SRA |
SRX2144134 |
