|
| Status |
Public on May 01, 2024 |
| Title |
8175_5 |
| Sample type |
SRA |
| |
|
| Source name |
Hepa1-6
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Hepa1-6
cell type: mouse hepatocarcinoma cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
8175_5
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...
|
| |
|
| Submission date |
Nov 08, 2023 |
| Last update date |
May 01, 2024 |
| Contact name |
Huichen Song |
| E-mail(s) |
DG1830025@smail.nju.edu.cn
|
| Phone |
15150516380
|
| Organization name |
Nanjing university
|
| Street address |
Qixia District, Xianlin Road No.163
|
| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210000 |
| Country |
China |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE247265 |
Burdock miR8175 improves insulin sensitivity in DIO mice by targeting PTP1B and PTPRF [I] |
| GSE248827 |
Burdock miR8175 improves insulin sensitivity in DIO mice by targeting PTP1B and PTPRF |
|
| Relations |
| BioSample |
SAMN38154630 |
| SRA |
SRX22415698 |
