|
Status |
Public on Jun 23, 2013 |
Title |
ribo-zero-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 |
Ribo-Zero 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 |
SRX254851 |
BioSample |
SAMN01990910 |