|
| Status |
Public on Sep 24, 2021 |
| Title |
Liver sinusoidal endothelial cells : CH1 |
| Sample type |
SRA |
| |
|
| Source name |
CCL4 treated rat_LSECs
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain background: Wistar Han
treatment/group: CCL4 treated rat
cell type: liver sinusoidal endothelial cells (LSECs)
|
| Growth protocol |
After liver tissue perfusion and digestion, LSECs were isolated by differential centrifugation protocol using iodixanol as density gradient medium.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Rat LSECs were collected with QIAzol lysis reagent (79306, Qiagen, MA, USA) for RNA extraction using miRNeasy microkit (74004, Qiagen, DE) for subsequent RNA sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Liver sinusoidal endothelial cells from CCL4 treated rat :CH1
|
| Data processing |
Raw reads data were converted into FASTQ format and quality control was performed using the FASTQC software (Babraham Bioinformatics).
After trimming for adapters using trim_galore (Babraham Bioinformatics), mapping of the reads were obtained using the STAR program against human genome (Rnor6) and the quantification of genes and transcripts were done with the RSEM program using ENSEMBL v91.
We use TMM method and limma-voom transformation from rounded expected counts to normalize the non biological variability
Genome_build: Rattus norvergicus(Rnor 6.0)
Supplementary_files_format_and_content: RSEM expected counts
|
| |
|
| Submission date |
Jan 14, 2021 |
| Last update date |
Sep 24, 2021 |
| Contact name |
Juanjo Lozano |
| E-mail(s) |
[email protected]
|
| Organization name |
CIBEREHD
|
| Department |
Plataforma de Bioinformatica
|
| Street address |
C/ Rosselló 153
|
| City |
Barcelona |
| ZIP/Postal code |
08036 |
| Country |
Spain |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE164878 |
Rat transcriptomic profiling of liver sinusoidal endothelial cells during chronic liver disease reveals stage-specific secretory signature |
|
| Relations |
| BioSample |
SAMN17319542 |
| SRA |
SRX9854721 |
