|
| Status |
Public on Dec 31, 2018 |
| Title |
EoE-D3 |
| Sample type |
SRA |
| |
|
| Source name |
EoE_distal esophagus
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
disease: eosinophilic esophagitis
tissue: Esophageal biopsies
location: distal esophagus
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TriZol
Illumina TruSeq RNA sample prep kit using barcodes for mulitplexing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
processed data file: EoE_GERDvsControl_Distal_AllGenes.txt
|
| Data processing |
Fastq data files aligned to human Hg19 genome with Bowtie short read aligner version 0.12.7
Bowtie aligned sam files were parsed into binary point data files and differentially expressed genes identified using the RNASeq application from USeq software version 7.8.
RNASeq application calculates fraction of reads that are exonic, intronic and intergenic and makes normalized read data tracks (RPKM) from the point data for visualization in the Integrated Genome Browser.
RNASeq application runs MultipleReplicaDefinedRegionScanSeqs (MRDRSS) for calculating differential expression using Anders DESeq negative binomial statistics and Benjamini and Hochberg mulitple testing correction.
Disease specific unannotated (novel) RNAs were identified using Cufflinks and Cuffcompare software and differential expression calcuated using MRDRSS application.
Genome_build: Human Hg19
Supplementary_files_format_and_content: text files with individual sample RPKM values, fold change and false discovery rate
|
| |
|
| Submission date |
Oct 18, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Don Delker |
| E-mail(s) |
don.delker@hsc.utah.edu
|
| Organization name |
University of Utah
|
| Department |
School of Medicine
|
| Street address |
30 North 1900 East
|
| City |
Salt Lake City |
| State/province |
Utah |
| ZIP/Postal code |
84132 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (1) |
| GSE41687 |
Novel genes differentiating Eosinophilic Esophagitis (EoE) from GERD identified by RNA Sequencing |
|
| Relations |
| SRA |
SRX197318 |
| BioSample |
SAMN01768006 |
