 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 11, 2016 |
| Title |
NH41 |
| Sample type |
SRA |
| |
|
| Source name |
P510.5
|
| Organism |
Homo sapiens |
| Characteristics |
patient: P510
diagnosis: Ulcerative colitis
prognosis: Pouchitis
tissue: Ileal pouch
biopsytime: 4mo
age: 51
Sex: female
ethnicity: Caucasian
|
| Extracted molecule |
total RNA |
| Extraction protocol |
clinical demographics: Patients were recruited for the prospective SHARE study at University of Chicago Medical Center and Mayo Clinic Rochester. Ulcerative colitis patients who underwent total proctocolectomy with IPAA and over the age of 18 were eligible for the study.
sample collection: biopsy via pouchoscopy
Total RNA was isolated using the AllPrep DNA/RNA Mini Kit (QIAGEN, Cat No. 8020). RNA quality was evaluated using Bioanalyzer (Agilent, Santa Clara, CA). All RNA samples displayed RNA Integrity Number (RIN) >7.
RNAseq including cDNA library preparation was processed at the Genomics Core Facility of University of Chicago (https://fgf.uchicago.edu/). Total RNA in the amount of 100-500μg per sample was depleted of ribosomal RNA using the Ribo-Zero kit (Epicentre, Madison, WI). The directional (first strand) cDNA libraries were prepared following the guide of TruSeq Stranded Total RNA Sample Preparation kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
biopsy
|
| Data processing |
Quality check of raw reads by FastQC
Tophat v2.0.10 for reads alignment and counts summary
Reads count data were processed using R/Bioconductor "limma" package for RPKM and 'voom' normalization
Batch effect resulted from two library preps were adjusted using "combat" function implemented in R/Bioconductor "sva" package
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include RPKM followed by ''voom' normalized and batch effect adjusted values
|
| |
|
| Submission date |
May 10, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Yong Huang |
| E-mail(s) |
[email protected]
|
| Phone |
(434) 243-0842
|
| Organization name |
University of Viginia
|
| Department |
Medicine
|
| Street address |
1340 Jefferson Park Ave
|
| City |
Charlottesville |
| State/province |
VA |
| ZIP/Postal code |
22908 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE81266 |
Ileal pouch transcriptomics reveal shared pathogenesis between pouchitis and ulcerative colitis |
|
| Relations |
| BioSample |
SAMN04966230 |
| SRA |
SRX1753717 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
