|
| Status |
Public on May 14, 2019 |
| Title |
Experiment 2 Native tdTomato hepatocytes – RED 3 |
| Sample type |
SRA |
| |
|
| Source name |
Native injured tdTomato hepatocytes
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
cell type: primary liver cells - hepatocytes
genotype: OPN-CreERT2;Rosa26R-mT/mG
liver status: Chronic injury
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction protocol not provided.
Libraries of experiment 1 were prepared starting from 150 ng of total RNA and using the TruSeq Stranded mRNA kit (Illumina, San Diego, CA) following the standard protocol (Part#15031047 Rev.E). Libraries of experiment 2 were constructed by starting from 150 ng of total RNA and using the KAPA RNA HyperPrep Kit with RiboErase (HMR) kit(KAPA Biosystems) according to manufacturer’s recommendations (KR1351 – v1.16)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Experiment 2 Sample 5
processed data file:
Experiment2.txt
RNA-16w3Red_S50
|
| Data processing |
Samples were quantified with kallisto v0.43.1 to obtain transcript counts
using a default kmer length of 31 and an index constructed from the Ensembl Mus musculus GRCm38 cDNA transcriptome dataset.
For each library, transcript counts were consolidated into counts-per-gene using the R/BIOCONDUCTOR package tximport v1.4.03
Genome_build: Mus musculus GRCm38 cDNA
Supplementary_files_format_and_content: The values in the matrix were produced by Kallistov0.43.1 using a default kmer length of 31 and an index constructed from the Ensembl Mus musculus GRCm38 cDNA transcriptome dataset. For each library, transcript counts were consolidated into counts-per-gene using the R/BIOCONDUCTOR package tximport v1.4.0.3.
|
| |
|
| Submission date |
May 14, 2018 |
| Last update date |
May 14, 2019 |
| Contact name |
Jérôme Ambroise |
| E-mail(s) |
jambroise83@gmail.com
|
| Organization name |
Université catholique de Louvain
|
| Department |
Institut de Recherche Expérimentale et Clinique
|
| Street address |
Avenue Hippocrate 54
|
| City |
Woluwé |
| ZIP/Postal code |
1200 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE114436 |
RNA sequencing in hepatocytes and DR-derived hepatocytes |
|
| Relations |
| BioSample |
SAMN09207628 |
| SRA |
SRX4082133 |
