|
| Status |
Public on Jul 25, 2023 |
| Title |
AKT+NICD RNA-seq rep3 |
| Sample type |
SRA |
| |
|
| Source name |
C57BL/6 WT
|
| Organism |
Mus musculus |
| Characteristics |
gender: Male
strain background: C57BL/6
age: 10-13 weeks
tissue: Liver
genotype/variation: AKT+NICD mouse
|
| Treatment protocol |
Sleeping beauty tranposone containing plasmids along with the transposase in a ratio of 25:1 were diluted in 2 ml of normal saline (0.9% NaCl), filtered through 0.22mm filter (Millipore), and hydrodynamically injected into the lateral tail vein of mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from mouse liver with miRNeasy Mini Kit (Qiagen) followed by manufacturer’s instructions.
RNA samples from livers were used to generate library using TruSeq kit from Illumina
We used in-house HiSeq2500 platform and sequenced 200 million reads to accurately quantify genes & transcripts
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were mapped to the mouse genome build mm10 using HISAT (Kim et al. 2015), and gene expression was normalized and quantified using HTSEQ default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using Python
|
| |
|
| Submission date |
Feb 25, 2020 |
| Last update date |
Jul 25, 2023 |
| Contact name |
Shuchang Liu |
| E-mail(s) |
shl96@pitt.edu
|
| Organization name |
University of Pittsburgh
|
| Street address |
203 Lothrop Street
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15261 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE145900 |
NOTCH-YAP1/TEAD-DNMT1 axis drives hepatocyte reprogramming into intrahepatic cholangiocarcinoma [RNA-Seq] |
| GSE200472 |
NOTCH-YAP1/TEAD-DNMT1 axis drives hepatocyte reprogramming into intrahepatic cholangiocarcinoma |
|
| Relations |
| BioSample |
SAMN14206561 |
| SRA |
SRX7799908 |
