|
| Status |
Public on Jul 01, 2019 |
| Title |
HACY_CD24 rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HACY_CD24+ liver progenitor cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 6-8 weeks
cell type: hepatocytes
cell subtype: MACS-sorted CD24+ cells
treatment: a cocktail of small molecules Y-27632, A-83-01, and CHIR99021 (HACY)
|
| Treatment protocol |
8-week-old mice were i.p. injected with CCL4 (2 ml/kg, Sigma-Aldrich) dissolved in olive oil at a ratio of 1:4 twice a week for 6 weeks.HACY treatment groups were intraperitoneally injected three times a week for 6 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Total RNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA)
The paired-end libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
HACY_CD24_1
|
| Data processing |
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Then the clean reads were mapped to reference genome using hisat2.
FPKM value of each gene was calculated using cufflinks.
and the read counts of each gene were obtained by htseq-count.
DEGs were identified using the DESeq (2012) R package functions estimate Size Factors and nbinomTest.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample
|
| |
|
| Submission date |
Jan 15, 2019 |
| Last update date |
Jul 02, 2019 |
| Contact name |
yan hexin |
| E-mail(s) |
hexinyw@163.com
|
| Organization name |
Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine
|
| Street address |
No. 1630 East Road
|
| City |
shanghai |
| ZIP/Postal code |
200120 |
| Country |
China |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE125095 |
Chemically Induced CD24+ hepatocyte-derived liver progenitor-like cells revert chronic hepatic dysfunction |
|
| Relations |
| BioSample |
SAMN10744215 |
| SRA |
SRX5250609 |
