|
Status |
Public on Oct 18, 2016 |
Title |
102842-001-048 |
Sample type |
SRA |
|
|
Source name |
EAC celline FLO-1LM cells
|
Organism |
Homo sapiens |
Characteristics |
cell line: FLO-1LM
|
Extracted molecule |
total RNA |
Extraction protocol |
Cells were harvested at 80% confluency, 24 hr after a media change. Total RNA was extracted using the Qiagen RNeasy Kit. RNA quality was confirmed using a Fragment AnalyzerTM (Advanced Analytical Technologies). cDNA library preparation was performed using the NEBNext Ultra directional RNA library Prep Kit (Illumina). DNA sequencing was conducted on the Illumina NextSeq 500 system.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
Image analysis, base calling and quality checks were undertaken with the Illumina data analysis pipeline RTA v2.4.11 and Bcl2fastq v2.17. Read data was mapped to the reference sequence Homo_sapiens.GRCh37.75 using a short read aligner after trimming for adapter sequences with Trimmomatic v0.30. A default mismatch rate of 2% was used. Genome_build: Homo_sapiens.GRCh37.75 Supplementary_files_format_and_content: File for every sample with scores representing read counts per gene
|
|
|
Submission date |
Oct 17, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Sanne Hoefnagel |
Organization name |
Academic Medical Centre Amsterdam
|
Department |
Gastroenterology
|
Lab |
CEMM Krishnadath
|
Street address |
Meibergdreef 9
|
City |
Amsterdam |
State/province |
Noord-Holland |
ZIP/Postal code |
1105AZ |
Country |
Netherlands |
|
|
Platform ID |
GPL18573 |
Series (1) |
GSE88802 |
Novel metastatic models of human esophageal adenocarcinoma highlight the importance of E-cadherin in cancer metastasis |
|
Relations |
BioSample |
SAMN05913786 |
SRA |
SRX2248680 |