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Sample GSM1173237 Query DataSets for GSM1173237
Status Public on Oct 21, 2013
Title normal esophagus
Sample type SRA
Source name snap frozen tissue of matched normal esophagus
Organism Homo sapiens
Characteristics disease state: esophageal adenocarcinogenesis
tissue: snap frozen tissue of normal esophagus
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: NE
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
BioSample SAMN02213924
SRA SRX315161

Supplementary file Size Download File type/resource
GSM1173237_NE.txt.gz 626.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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