|
| Status |
Public on Oct 21, 2013 |
| Title |
esophageal adenocarcinoma |
| Sample type |
SRA |
| |
|
| Source name |
snap frozen tissue of matched esophageal adenocarcinoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: esophageal adenocarcinogenesis
tissue: snap frozen tissue of esophageal adenocarcinoma cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from snap frozen tissues using a Qiagen RNeasy Plus Mini Kit (Qiagen, Valencia, CA).
An adaptor ligated cDNA library was prepared from the sample RNAs using Illumina® TruSeq® RNA Sample Preparation Kit v2 (Illumina Inc., San Diego, CA). The resulting libraries were sequenced using Illumina HiSeq 2500 sequencer (single-end reads).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample name: EAC
|
| Data processing |
Initial processing of data was done by the Illumina Sequence Control Software (SCS) and Pipeline 1.n software packages. These software components perform the functions of image analysis (Firecrest), base-calling (Bustard) and alignment of sequence tags to the Appropriate reference genome (ELAND), sorting samples by the index sequences (up to 4 per lane). Differential expression analysis between samples was performed by edgeR, a bioconductor package specifically for the analysis of replicated count-based expression data (Robinson MD et al., 2010).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: The tab-delimited .txt files include normalized gene expression (abundance of all genes that were detected, including lncRNAs) for each Sample.
|
| |
|
| Submission date |
Jun 24, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Yiting Yu |
| Organization name |
Albert Einstein College of Medicine
|
| Street address |
1300 Morris Park Ave
|
| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE48240 |
Long Noncoding RNA HNF1A-AS1 Regulates Proliferation and Migration in Esophageal Adenocarcinoma Cells |
|
| Relations |
| BioSample |
SAMN02213923 |
| SRA |
SRX315160 |
