|
| Status |
Public on Feb 01, 2019 |
| Title |
EAC RNA-Seq #2 |
| Sample type |
SRA |
| |
|
| Source name |
EAC primary specimen
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: esophagus
region: epithelium
developmental stage: adult
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol reagent (Invitrogen/Life Technologies #15596-026).
Libraries were prepared according to instructions forIllumina RNA-Seq library preparation kit with Ribozero.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed with Illumina RTA version 1.12.4.2
Raw read counts were normalized with DESeq
Reads were aligned to the hg19 genome with Tophat.
Cuffdiff v2.1.1 was applied to analyze the differential gene expression between EAC and control (SQ) using a log2(fold change) of 1.0 as a cut-off for gene experssion.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited cuffdiff output file includes sample gene FPKMs and gene-level differential expression.
|
| |
|
| Submission date |
Feb 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Chin-Hsing Annie Lin |
| Organization name |
University of Texas at San Antonio
|
| Department |
Biology
|
| Lab |
BSB2.03.24
|
| Street address |
One UTSA Circle
|
| City |
San Antonio |
| State/province |
TX |
| ZIP/Postal code |
78249 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE94544 |
Epigenetic repression via DNA methylation and trimethylation of H3K27 alters gene expression in esophageal adenocarcinoma [RNA-Seq] |
| GSE94545 |
Epigenetic repression via DNA methylation and trimethylation of H3K27 alters gene expression in esophageal adenocarcinoma |
|
| Relations |
| BioSample |
SAMN06299373 |
| SRA |
SRX2539421 |
