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Sample GSM1616964 Query DataSets for GSM1616964
Status Public on Jul 15, 2015
Title B1/non-strituring, non-penetrating Crohn's disease [ncRNA-Seq, 408_CD_NI_B1]
Sample type SRA
 
Source name Colon
Organism Homo sapiens
Characteristics age: 23
Sex: female
disease: Crohn's Disease
disease_stage: B1/non-strictuing, non-penetrating
inflamed: No
montreal classification: A2L2B1
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 SAMN03366630
SRA SRX886306

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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