|
| Status |
Public on Jun 23, 2013 |
| Title |
poly-A-SNU-719 |
| Sample type |
SRA |
| |
|
| Source name |
Gastric carcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: gastric carcinoma cell line SNU-719
passage: 3-5
infection: EBV
|
| Growth protocol |
Cells were grown in RPMI supplemented with 10% FBS in a humidified chamber with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Trizol protocol.
Two separate cDNA libraries were prepared from polyA selected and from Ribo-Zero selected RNAs using the Illumina Truseq Stranded Total RNA Sample Prep Kit (RS-122-2101).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Poly-A selected RNA
|
| Data processing |
alignments to hg19 (UCSC) using novoalign (v.2.08.02) using default settings
read counts were calculated using HT-seq count using the interesection-strict option and the GRCh37.70 annotation file.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample
|
| |
|
| Submission date |
Mar 24, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Erik K Flemington |
| E-mail(s) |
eflemin@tulane.edu
|
| Phone |
504 988-1167
|
| Organization name |
Tulane Health Sciences Center
|
| Department |
Pathology
|
| Street address |
1430 Tulane Ave., SL79
|
| City |
New Orleans |
| State/province |
LA |
| ZIP/Postal code |
70112 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE45453 |
Differences in gastric carcinoma microenvironment stratify according to EBV infection intensity; implications for possible immune adjuvant therapy |
|
| Relations |
| SRA |
SRX254850 |
| BioSample |
SAMN01990909 |
