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Sample GSM2348284 Query DataSets for GSM2348284
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
BioSample SAMN05913786
SRA SRX2248680

Supplementary file Size Download File type/resource
GSM2348284_102842-001-048.count.txt.gz 210.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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