|
| Status |
Public on Dec 25, 2018 |
| Title |
Liver from C57 mice number 3 with BDL and anti-miR-873 treated |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57
age: 3 month
treatment: anti-miR-873 treated
|
| Growth protocol |
Mice were breed and housed at the Animal Facility of CIC bioGUNE under controled conditions according to the animal care international gidelines.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from the livers using TRIZOL reagent (Invitrogen)
TruSeq® RNA Sample Preparation v2 (Illumina Inc.)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
NO_BDL_vs_anti873.tsv
miR_Ctrl_vs_anti873.tsv
anti_873_3
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Individual FASTQ files for each sample were merged prior to the quality control & filtering steps
Quality control of the reads was carried out using FASTQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were filtered from the adapter sequences and their quality score using trim_galore software. (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and only are retained those with at least 20 phred quality score.
Reads were mapped to mm10 (Mus musculus) reference genome using Tophat (https://ccb.jhu.edu/software/tophat/index.shtml) toaccount for spliced reads alignments, allowing two mismatches (n = 2).
Resulting BAM aligment files were used in as input for a Differential Expression Analysis pipeline based on DESeq2 BioconductoR package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: mm10
Supplementary_files_format_and_content: Tables of raw counts, obtained from the SAM files of the samples in each comparative. These tables are in tab separated plain text format.
|
| |
|
| Submission date |
Feb 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jose Luis Lavin |
| E-mail(s) |
joluito@gmail.com
|
| Organization name |
CIC bioGUNE
|
| Street address |
Parque Tecnológico de Bizkaia Building 502, Floor 0
|
| City |
Derio |
| State/province |
Bizkaia |
| ZIP/Postal code |
48160 |
| Country |
Spain |
| |
|
| Platform ID |
GPL16173 |
| Series (1) |
| GSE77840 |
Gene expression analysis of mouse liver after bile duct ligation (BDL) treated or not with anti-miR-873 |
|
| Relations |
| SRA |
SRX1571348 |
| BioSample |
SAMN04501158 |
