|
| Status |
Public on Jul 15, 2015 |
| Title |
B3/penetrating Crohn's disease [RNA-Seq, 29_CD_NI_B3] |
| Sample type |
SRA |
| |
|
| Source name |
Colon
|
| Organism |
Homo sapiens |
| Characteristics |
age: 59
Sex: female
disease: Crohn's Disease
disease_stage: B3/penetrating
inflamed: No
montreal classification: A2L3B3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from fresh-frozen human colon tissues using the Qiagen RNeasy Mini Kit
mRNA libraries were generated using Illumina TruSeq polyA+ Sample Prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were trimmed to 50 bp
Reads were filtered on the criteria that 90% of bases within the read have quality >= 20
Potential artifactual reads from Truseq library were filtered using tagdust with an fdr cutoff of 0.001
Reads were aligned to personal genomes using GSNAP alignment software, taking into account known heterozygous sites within each individual.
Raw gene counts were derived using a custom perl script and exon annotation gtf file downloaded from UCSC Table Browser
Normalized gene counts were obtained using the varianceStabilizingTransformation function in the R package "DEseq", with default parameters
genome build: hg19
Supplementary_files_format_and_content: Raw/Normalized read counts
|
| |
|
| Submission date |
Feb 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Bailey Peck |
| E-mail(s) |
bpeck@email.unc.edu
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Genetics
|
| Lab |
Sethupathy
|
| Street address |
120 Mason Farm Rd, 5100H Genetic Medicine Bldg
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE66207 |
mRNA and small RNA associated with Crohn's disease behavior [RNA-Seq] |
| GSE66209 |
mRNA and small RNA associated with Crohn's disease behavior |
|
| Relations |
| BioSample |
SAMN03366648 |
| SRA |
SRX886253 |
