|
| Status |
Public on Mar 14, 2018 |
| Title |
Bone marrow-derived macrophages Bb-stimulated 2 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Bone marrow-derived macrophages
strain: C57BL/6(h-2b)
age: 8 weeks
treatment: Stimulated with Borrelia burgdorferi 297
|
| Treatment protocol |
Macrophages were stimulated with Borrelia burgdorferi strain 297 at a multiplicity of infection of 25.
|
| Growth protocol |
Mice were breed and housed at the Animal Facility of CIC bioGUNE under controled conditions according to the animal care international gidelines. Bone marrow-derived macrophages were collected from the femoral shafts and incubated in 100 mm x 15 mm petri dishes (Thermo Fisher Scientific) for 8 days in DMEM supplemented with 10% FCS, and 10% penicillin-streptomycin plus 30 ng/ml of M-CSF (Miltenyi Biotec, Bergisch Gladbach, GE). Following incubation, non-adherent cells were eliminated and adherent macrophages were scraped, counted and seeded in 6-well tissue-culture plates for stimulation at a density of 106 cells /ml.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the NucleoSpin® RNA kit (Macherey-Nagel, Düren, GE)
TruSeq® RNA Sample Preparation v2 (Illumina Inc.)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
WT2_Bb
|
| 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 BAM files of the samples in each comparative. These tables are in tab separated plain text format.
|
| |
|
| Submission date |
Sep 05, 2017 |
| 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 (2) |
| GSE103482 |
A multi-omic analysis reveals a regulatory role of CD180 during the response of macrophages to Borrelia burgdorferi [RNA-Seq] |
| GSE103483 |
A multi-omic analysis reveals a regulatory role of CD180 during the response of macrophages to Borrelia burgdorferi |
|
| Relations |
| BioSample |
SAMN07604958 |
| SRA |
SRX3160956 |
