 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 19, 2019 |
| Title |
BB608-1 |
| Sample type |
SRA |
| |
|
| Source name |
FaDu Cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HNSCC
treatment: BB608
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol
library preparation was done using Illumina TruSeq Stranded Total RNA (with Ribo-Zero Gold) preparation kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
RNA-Seq reads were mapped and aligned using Tophat (v2.0.11)
Aligned results were assambled using Cufflinks (v2.2.1) and fragment bias correction performed (Kasper et al,2010 and Adam et al., 2011)
Cuffdiff was used for group comparison and to calculate the FPKM
Post processing of Cufflinks and Cuffdiff was performed by using CummeRbund for data visualization
Genome_build: hg19
|
| |
|
| Submission date |
Feb 22, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Harry Rogoff |
| Organization name |
Boston Biomedical, Inc.
|
| Street address |
640 Memorial Dr.
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE78178 |
Effect of BB608 on Gene Expression in HNSCC Cell Line |
|
| Relations |
| BioSample |
SAMN04507522 |
| SRA |
SRX1596757 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
