|
| Status |
Public on Feb 01, 2016 |
| Title |
Low_Pt1_posterior_pleural |
| Sample type |
SRA |
| |
|
| Source name |
Lung tumor
|
| Organism |
Homo sapiens |
| Characteristics |
cancer type: Non-small cell lung cancer (NSCLC)
perfusion group: low
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Human tumor samples were hormogenized in Trizol and the total RNA was extracted using RNeasy Mini Kit (Qiagen) following the manufacturer's protocol.
1-3 ug of total RNA was processed for library generation using Ovation human FFPE RNA-Seq library systems (NuGen) following the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequencing reads were aligned to human genome assembly hg19 by TopHat.
Transcripts were assembled and the abundance was estimated by Cufflinks.
The number of reads aligned to RefSeq annotated genes' exons were counted and further normalized to be of unit of FPKM ( number of fragments per kilo base of exon per million reads mapped) by Cuffnorm.
Genome_build: hg19
Supplementary_files_format_and_content: text file of gene read count values
Supplementary_files_format_and_content: text file of gene FPKM values
|
| |
|
| Submission date |
Oct 29, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Min Ni |
| E-mail(s) |
min.ni@utsouthwestern.edu
|
| Organization name |
UT Southwestern Medical Center
|
| Department |
Children's Research Institute
|
| Lab |
DeBerardinis Lab
|
| Street address |
6000 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE74484 |
Gene expression profiling in metabolically heterogeneous human lung tumors |
|
| Relations |
| BioSample |
SAMN04225786 |
| SRA |
SRX1397802 |
