|
| Status |
Public on Jul 15, 2015 |
| Title |
B3/penetrating Crohn's disease [ncRNA-Seq, 450_CD_NI_B3] |
| Sample type |
SRA |
| |
|
| Source name |
Colon
|
| Organism |
Homo sapiens |
| Characteristics |
age: 28
Sex: female
disease: Crohn's Disease
disease_stage: B3/penetrating
inflamed: No
montreal classification: A2L1B3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from fresh-frozen human colon tissues using the Qiagen RNeasy Mini Kit
Small RNA libraries were generated using Illumina TruSeq Small RNA Sample Preparation Kit
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Small RNA-seq data was aligned using methodology described in Baran-Gale et al. (PLOS ONE, 2012)
Reads were trimmed by cutAdapt to remove adaptor remnants. Trimmed reads of 14-41 nt are first mapped exactly (no mismatches) using Bowtie. Windows are determined using these mapped reads, and the unmapped reads, are realigned to these windows using SHRiMP2 with mismatches allowed (See Baran-Gale et al, 2012), these would be considered edits & isomiRs, and are named based on the canonical miRNA (miRbase).
Reads were normalized using Reads per Million Mapped (RPMM). We pulled out miRNAs and isomiRs with at least 100 RPMM in at least 1 sample for downstream analyses.
Genome_build: Hg19
Supplementary_files_format_and_content: Multiple sample Tab-delimited file with RPMMs of all miRNAs & isomiRs that reached 100 RPMM in at least one sample analyzed.
|
| |
|
| 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) |
| GSE66208 |
mRNA and small RNA associated with Crohn's disease behavior [ncRNA-Seq] |
| GSE66209 |
mRNA and small RNA associated with Crohn's disease behavior |
|
| Relations |
| BioSample |
SAMN03366582 |
| SRA |
SRX886316 |
