|
| Status |
Public on Dec 30, 2019 |
| Title |
BX rep3 |
| Sample type |
SRA |
| |
|
| Source name |
stool
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129/SvEv
treatment: biofilm-negative
genotype: ApcMin/+;Il10-/-
|
| Treatment protocol |
biofilm-negative , biofilm-positive, no treatment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mirVana miRNA isolation kit
NEBNext Multiplex Small RNA Library Prep Set for Illumina kit (E7300, NEB)
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
CAP-miRSeq analysis: sequences were filtered and trimmed using cutadapt. Quantification of miRNA was done using miRDeep2 and differentially expressed miRNAs were detected using edgeR
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files of EdgeR normalized expression
|
| |
|
| Submission date |
Dec 15, 2017 |
| Last update date |
Dec 30, 2019 |
| Contact name |
Christian Jobin |
| Organization name |
University of Florida
|
| Department |
Medicine
|
| Street address |
2033 Mowry Rd, CGRC-461, PO Box: 103633
|
| City |
Gainesville |
| State/province |
Florida |
| ZIP/Postal code |
32610 |
| Country |
USA |
| |
|
| Platform ID |
GPL16417 |
| Series (2) |
| GSE108164 |
Microbial activities associated with human intestinal mucosal biofilms change mRNAs and microRNAs to promote carcinogenesis in mice [miRNA] |
| GSE108165 |
Microbial activities associated with human intestinal mucosal biofilms change mRNAs and microRNAs to promote carcinogenesis in mice |
|
| Relations |
| BioSample |
SAMN08183234 |
| SRA |
SRX3475170 |
