|
| Status |
Public on Oct 16, 2023 |
| Title |
KO_PP_22: Colon macrophages from MCJ deficient mice 8 Ant+DSS+ |
| Sample type |
SRA |
| |
|
| Source name |
Colon macrophages
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6(h-2b)
age: 8 weeks
tissue: Colon macrophages
|
| Treatment protocol |
Mice were treated with a broad spectrum antibiotic during 7 days or not previously to DSS treatment for 6 days. Mice colon tissue was collected and macrophages were extracted using several washing steps and by enzymatic disruption mediated by collagenase type IV.
|
| 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 |
Total RNA was extracted using Trizol reagent protocol.
Universal Plus mRNA-SeqNuGEN
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| 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 STAR v2.5.4 (https://github.com/alexdobin/STAR).
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 BAM files of the samples in each comparative using Rsubread BioconductoR package (http://bioconductor.org/packages/release/bioc/html/Rsubread.html). These tables are in tab separated plain text format.
|
| |
|
| Submission date |
Jul 29, 2019 |
| Last update date |
Oct 16, 2023 |
| 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) |
| GSE135033 |
Colon macrophage transcriptomes reveals the impact of mitochondrial dysfunction in ulcerative colitis |
|
| Relations |
| BioSample |
SAMN12390505 |
| SRA |
SRX6608738 |
