|
| Status |
Public on Feb 03, 2019 |
| Title |
Tumor tissue from ND mice,number 3 |
| Sample type |
SRA |
| |
|
| Source name |
hepatocellular carcinoma
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Hep1-6
culture condition: Hep1-6 cells were cultured in DMEM supplemented with 10% FBS,and then subcutaneously injected into C57BL/6J mice fed with normal diet.
strain: C57BL/6J
diet: normal diet (ND)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
Pairedend libraries were synthesized by using the TruSeq® RNA Sample Preparation Kit (Illumina, USA) following TruSeq® RNA Sample Preparation Guide.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
Tumor tissue from ND mice were harvested and total RNA were extracted
|
| Data processing |
Basecalls performed using CASAVA version 1.8.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Seqtk.
mRNA-seq reads were aligned to the mm10 genome assembly using TopHat(version:2.0.9)
Gene abundance measurements were generationed and normalized using HTSeq. The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM).
Differential expression were analysed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
|
| |
|
| Submission date |
Jan 03, 2019 |
| Last update date |
Feb 03, 2019 |
| Contact name |
Fu jing |
| Organization name |
Eastern Hepatobiliary Surgery Hospital
|
| Department |
Liver Centre of SMMU
|
| Lab |
International Cooperation Laboratory on Signal Transduction
|
| Street address |
No.225 Changhai road
|
| City |
shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE124599 |
RNA-seq data for tumor tissues from mice fed with normal diet (ND) or high cholesterol diet (HCD) [Hep1-6] |
|
| Relations |
| BioSample |
SAMN10688922 |
| SRA |
SRX5197730 |
