|
| Status |
Public on Oct 18, 2016 |
| Title |
102842-001-051 |
| Sample type |
SRA |
| |
|
| Source name |
EAC celline FLO-1 parental cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: FLO-1 parental
|
| 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 |
SAMN05913787 |
| SRA |
SRX2248683 |
