|
| Status |
Public on Aug 24, 2017 |
| Title |
MKO+CCl4_3 |
| Sample type |
SRA |
| |
|
| Source name |
hepatic F4/80+ cells
|
| Organism |
Mus musculus |
| Characteristics |
background strain: C57BL/6
genotype: KO
tissue: liver
cell type: macrophage
gender: male
age: 3 months
|
| Treatment protocol |
mice were administered intraperitonneal carbon tetrachloride to induce experimental fibrosis
|
| Growth protocol |
3 month old male mice were used for the experiment and maintained on normal chow
|
| Extracted molecule |
total RNA |
| Extraction protocol |
liver of treated mice were digested and F4/80+ cells were immunoselected by magnetism-assisted cell sorting, mRNA was isolated by silica membrane spin columns
Messenger (polyA+) RNAs were purified from 30 ng of total RNA using oligo(dT). Libraries were prepared using the strand specific RNA-Seq library preparation TruSeq Stranded mRNA kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina Bcl2fastq2 2.17 software used for basecalling.
Before mapping, poly N read tails were trimmed, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded. Reads were then aligned against the genome using STAR (version 2.4.0k)
Alignments from reads matching more than once on the reference genome were removed using Java version of samtools
To compute gene expression, GRCm38.p4 GFF3 genome annotation version 81 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq-count 0.5.3
The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3
Genome_build: GRCm38.p4 Ensembl version 81
Supplementary_files_format_and_content: DESeq 1.8.3 normalized counts
|
| |
|
| Submission date |
Jun 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephane Le Crom |
| Organization name |
IBENS
|
| Department |
Genomic Core Facility
|
| Street address |
46 rue Ulm
|
| City |
PARIS |
| ZIP/Postal code |
75230 |
| Country |
France |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE82157 |
Murine myeloid response to experimental fibrosis |
|
| Relations |
| BioSample |
SAMN05198120 |
| SRA |
SRX1816658 |
