|
| Status |
Public on Nov 06, 2018 |
| Title |
AAA0500929 [miRNA-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
D29
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: intestinal tissue
disease state: ulcerative colitis
group: patients with active ulcerative colitis before receiving glucocorticoids and who will have a poor response to treatment (non-responders, NR)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
miRNeasy Mini Kit (QIAGEN)
TruSeq Small RNA Sample Prep Kit (Illumina Inc.)
Isolation of mature microRNA fraction
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
G3_intestinal samples from patients with active ulcerative colitis before receiving glucocorticoids and who will have a poor response to treatment (non-responders, NR)
|
| Data processing |
Quality Control: performed by an in-house written quality control function, axShortReadQCAnax. This function formats and filters the reads based of their per-base reported quality
Adapters removing: using Trimmomatic v 0.32.
Alignment: aligned to miRBase v21 mature miRNA sequences using Bowtie 2 with parameters '--local','-L 16'
The raw mapping data was filtered for uniquely mapped reads using SAMtools.
Feature Count
Expression normalization and Differential expression analysis using R bioconductor packages EdgeR and Limma
Genome_build: mature miRNAs (miRBase version 21)
Supplementary_files_format_and_content: tab-delimited text file of raw counts for mature miRNAs (miRBase version 21) across samples. Tab delimited text files of edger , limma (voom) normalized counts
|
| |
|
| Submission date |
May 17, 2018 |
| Last update date |
Nov 06, 2018 |
| Contact name |
Ana Maria Aransay |
| E-mail(s) |
amaransay@cicbiogune.es
|
| Phone |
0034944061325
|
| Organization name |
CIC bioGUNE
|
| Department |
Genome Analysis Platform
|
| Street address |
Parque tecnologico de Bizkaia, Building 801-A
|
| City |
Derio |
| State/province |
BIZKAIA |
| ZIP/Postal code |
48160 |
| Country |
Spain |
| |
|
| Platform ID |
GPL15456 |
| Series (2) |
| GSE114591 |
A systems biology approach identifies ANP32E and other biomarkers of glucocorticoid refractoriness in ulcerative colitis [miRNA-Seq] |
| GSE114603 |
A systems biology approach identifies ANP32E and other biomarkers of glucocorticoid refractoriness in ulcerative colitis |
|
| Relations |
| BioSample |
SAMN09220991 |
| SRA |
SRX4095952 |
