|
| Status |
Public on Aug 14, 2019 |
| Title |
Liver Hepatocyte in WT condition Hepatocyte-WT-4 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
|
| Treatment protocol |
All Methods listed in Bonnardel et al. Stellate cells, hepatocytes and endothelial cells imprint the Kupffer cell identity on monocytes colonizing the liver macrophage niche . Immunity. 2019.
|
| Growth protocol |
All Methods listed in Bonnardel et al. Stellate cells, hepatocytes and endothelial cells imprint the Kupffer cell identity on monocytes colonizing the liver macrophage niche . Immunity. 2019.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
All Methods listed in Bonnardel et al. Stellate cells, hepatocytes and endothelial cells imprint the Kupffer cell identity on monocytes colonizing the liver macrophage niche . Immunity. 2019.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Liver Hepatocyte in WT condition
Liver Hepatocyte in WT condition
|
| Data processing |
FastQC v0.11.4 is used to check the quality of the samples
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic v0.35 with parameters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:35
Sequenced reads were then mapped to mm10 transcriptome using Tophat2 v2.1.0 with parameters --library-type fr-unstranded --min-intron-length 50 --no-coverage-search
The mapping files were then filtered using samtools v0.1.18 (samtools view with parameters -bq 20) and sorted using samtools sort
Reads were counted using HTSeqCount v0.6.1p1 with parameters -f bam -m intersection-strict -s no -a 10 -t exon -i gene_id
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw counts (output HTSeqCount) for each sample
|
| |
|
| Submission date |
Aug 13, 2019 |
| Last update date |
Aug 14, 2019 |
| Contact name |
Liesbet Martens |
| E-mail(s) |
liesbet.martens@irc.vib-ugent.be
|
| Organization name |
VIB-University of Ghent
|
| Department |
VIB Inflammation Research Center
|
| Street address |
Technologiepark 927
|
| City |
Zwijnaarde |
| ZIP/Postal code |
9052 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE135789 |
Stellate cells, hepatocytes and endothelial cells imprint the Kupffer cell identity on monocytes colonizing the liver macrophage niche (RNA-Seq) |
| GSE135790 |
Stellate cells, hepatocytes and endothelial cells imprint the Kupffer cell identity on monocytes colonizing the liver macrophage niche |
|
| Relations |
| BioSample |
SAMN12567444 |
| SRA |
SRX6709172 |
