|
| Status |
Public on Aug 14, 2024 |
| Title |
S209A_1 24h Fast heavy polysome |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
Sex: Male
genotype: eIF4E S209A/S209A
treatment: Fast
time: 24h
|
| Treatment protocol |
For studying fasting, food was removed from mice for 24h. Fed mice were available to food all the time.
|
| Growth protocol |
Wild type or eIF4E S209A/S209A C57BL/6 mice were were maintained under pathogen-free conditions and all experiments were performed in compliance with guidelines approved by the Institutional Animal Care and Use Committee of UCSF.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were seperated using sucrose gradient, and fractions 2-7, and 8-13 were pulled together, same amout of ERCC was added to each pool, PureLink™ RNA Mini Kit (ThermoFisher). 10ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Galaxy server at the University of Manchester (https://centaurus.itservices.manchester.ac.uk/)
Sequence reads were trimmed with Trimmomatic.
Trimmed reads were aligned to the mouse genome (Version mm10) using HISAT2
Counts were calculated using Stringtie and annotated using GENCODE.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
May 11, 2023 |
| Last update date |
Aug 14, 2024 |
| Contact name |
Haojun Yang |
| E-mail(s) |
haojun.yang@ucsf.edu
|
| Organization name |
UCSF
|
| Lab |
Ruggero lab
|
| Street address |
1450 3rd Street
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE232342 |
Translation efficiency in the mouse liver upon 24h fasting |
|
| Relations |
| BioSample |
SAMN35051818 |
| SRA |
SRX20301529 |
