|
| Status |
Public on Jan 11, 2016 |
| Title |
PDX4_RIBA1 |
| Sample type |
SRA |
| |
|
| Source name |
De-identified patient derived xenograft, passage 4
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: PDX cells
treatment: 80mg/kg/b.i.d ribavarin IP for 10 days
growth protocol: PDX was established in NSG mice for 4 passages
basecalling: CASAVA 1.8.2
alignment tool: STAR
differential expression tool: EdgeR
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was harvested with Trizol reagent (Life Technologies).
Genomic DNA was eliminate with Dnase treatment, and mRNA was isolated using two rounds of poly-T oligo attached magnetics beads. Sequencing libraries were generated with the Illumina TruSeq RNA sample prep kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
topTags_Ribavarin-Control.txt
PDX_RIBA-CON_counts
|
| Data processing |
Illumina Casava1.8.0 or 1.8.2 software used for basecalling.
Reads that passed filter were aligned to hg19 using TopHat (Trapnell et al., 2009) or STAR (Dobin et al., 2012).
Gene expression values were estimated with Cufflinks (V1.3.0, Trapnell et al., 2010) or were calculated by counting how many reads map uniquely to the union of all gene exons using HTseq-count (http://www.huber.embl.de/users/anders/ HTSeq/).
Differentially expressed genes were identified with cuffdiff time series (LY1 samples) or the edgeR package (Robinson et al., 2010, PDX samples). Genes with a FDR-corrected p-value < 0.05 were considered differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: The normalized abundance measurements and differential expression testing given by Cuffdiff are both provided as .txt files. Read counts that map uniquely to the union of all gene exons using HTseq-count and the EdgeR output are provided as a .txt file.
|
| |
|
| Submission date |
Nov 13, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Tharu M Fernando |
| E-mail(s) |
tmf2001@med.cornell.edu
|
| Phone |
646-962-6728
|
| Organization name |
Weill Cornell Medical College
|
| Department |
Medicine, Heme-Onc
|
| Lab |
Ari Melnick
|
| Street address |
413 East 69th St BB1462
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE63265 |
Combinatorial targeting of nuclear export and translation of RNA inhibits aggressive B-cell lymphoma |
|
| Relations |
| BioSample |
SAMN03177904 |
| SRA |
SRX758626 |
