|
| Status |
Public on Aug 06, 2020 |
| Title |
iHep_4a2_1 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic fibroblasts
strain: C57BL/6
transfection: infected with Foxa2, Hnf4alpha
Stage: iHep
|
| Treatment protocol |
Retrovirus was produced following standard procedures, following transfection of pGCDNsam retroviral backbones containing the respective cDNAs (available from us via Addgene). Media was changed 8 hours after transfection and viral supernatant collected after another 24 and 48 hours.
|
| Growth protocol |
Mouse embryonic fibroblasts (MEFs) were prepared from 13.5 days post coitum embryos. iHep cells were generated and maintained following the previously described protocol (Sekiya and Suzuki, 2011). Hepatocytes were isolated from 10-week-old adult mouse livers by two-step collagenase digestion (Seglen, 1979).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy Micro Kit (Qiagen)
RNA-seq libraries were prepared using the Illumina Truseq Stranded mRNA protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
The sequence reads were aligned to the mouse reference genome assembly (NCBI37/mm9) using bwa (v0.7.12) with the option (mem -t 6 -M)
Fragments per kilobase of exon per million mapped fragments (FPKM) was calculated from the aligned reads by using Tigar (v2) with the default option
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample
|
| |
|
| Submission date |
Nov 25, 2016 |
| Last update date |
Aug 06, 2020 |
| Contact name |
Atsushi Suzuki |
| Organization name |
Kyushu University
|
| Department |
Medical Institute of Bioregulation
|
| Lab |
Division of Organogenesis and Regeneration
|
| Street address |
3-1-1 Maidashi, Higashi-ku
|
| City |
Fukuoka |
| State/province |
Fukuoka |
| ZIP/Postal code |
812-8582 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE90534 |
Transcriptome analysis of the induced hepatocyte-like (iHep) cells |
|
| Relations |
| BioSample |
SAMN06064775 |
| SRA |
SRX2379217 |
