|
| Status |
Public on May 01, 2016 |
| Title |
3691_DAPT_5um |
| Sample type |
SRA |
| |
|
| Source name |
Primary Patient Derived Tumor Model
|
| Organism |
Homo sapiens |
| Characteristics |
tumor model: 3691
treatment 1: 5uM DAPT
|
| Growth protocol |
See Individual Samples
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from ~1x10^6 cells 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 the CWRU Genomics Core using the Illumina stranded TruSeq RNA Sample Preparation Kit according to the manufacturer's protocol.
RNA-seq libraries were sequenced on the Illumina HiSeq 2500 platform at the Case Western Reserve University Genomics Core Facility.
|
| |
|
| 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 |
Mar 30, 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) |
| GSE79735 |
RNA-seq Profiles in RBPJ Maintains Brain Tumor Initiating Cells through CDK9-mediated Transcriptional Elongation |
| GSE79736 |
RBPJ Maintains Brain Tumor Initiating Cells through CDK9-mediated Transcriptional Elongation |
|
| Relations |
| BioSample |
SAMN04590824 |
| SRA |
SRX1670491 |
