|
| Status |
Public on Apr 01, 2017 |
| Title |
3565_culture_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Primary Patient Derived Tumor Model
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primary patient-derived GBM cells
|
| Growth protocol |
IN528 cells from a primary patient derived GBM tumor model were grown in serum free cell culture conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected and lysed in trizol
RNA was extracted with TRIzol (Invitrogen), separated using Phase Lock Gel tubes (5 Prime), and purified using the miRNAeasy kit (Qiagen) according to the manufacturer’s protocol.
Total RNA was prepared for sequencing by Beckman-Coulter Genomics using the Illumina TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer's protocol.
RNA-seq libraries were sequenced on the Illumina HiSeq 2500 platform by Case Western Genomics Core
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
For gene expression analysis, reads were aligned to the hg19 genome build (retrieved from http://cufflinks.cbcb.umd.edu/igenomes.html), using Tophat v2.0.6 (Trapnell et al., 2009).
The distribution of alignments was analyzed using the CollectRnaSeqMetrics module of Picard v1.89 (http://picard.sourceforge.net/).
FPKM values for known genes were calculated using Cufflinks v2.0.2 (Trapnell et al., 2010) provided with the GTF file via the -G (known genes only) option. FPKM values were Quantile Normalized.
Genome_build: Hg19
Supplementary_files_format_and_content: FPKM values from Cufflinks
|
| |
|
| Submission date |
Oct 17, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Tyler E Miller |
| Organization name |
Cleveland Clinic Lerner Research Institute
|
| Department |
Stem Cell Biology and Regenerative Medicine
|
| Lab |
Jeremy Rich Lab
|
| Street address |
2111 E 96th Street, NE3-256
|
| City |
Cleveland |
| State/province |
Ohio |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE74516 |
RNA-seq Profiles in Transcription elongation factors are in vivo-specific cancer dependencies in glioma |
| GSE74529 |
Transcription elongation factors are in vivo-specific cancer dependencies in glioma |
|
| Relations |
| BioSample |
SAMN05914510 |
| SRA |
SRX2248855 |
