|
| Status |
Public on Jan 29, 2024 |
| Title |
Ctrl.AL.1 |
| Sample type |
SRA |
| |
|
| Source name |
hypothalamus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: hypothalamus
Sex: Male
strain: B6/J
genotype: Control
treatment: Ad Libitum Fed
timepoint: ZT16
|
| Treatment protocol |
Mice were fed ad libitum or fasted from ZT0 to ZT16.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Hypothalamus from coordinates: 0 to -3 mm anteroposterior, 1.5 to -1.5 mm mediolateral, 4 to 7 mm dorsoventral were dissected. Extraction was performed with Zymo total RNA columns.
polyA containing transcripts were enriched and library prepped by Novogene. Libraries were sequenced to ~20 million, paired-end, 150 bp reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
fastq files were aligned to mm10 genome using STAR (2.7.10b) indexer with default options
Reads from aligned files were assigned to genes using Subread::featurecounts (v2.0.1) with options -J, -M, -p, -g
Assembly: mm10
Supplementary files format and content: output of Subreads::featurecounts by gene. Reads per gene per library
|
| |
|
| Submission date |
Jan 24, 2024 |
| Last update date |
Jan 29, 2024 |
| Contact name |
Louis Ptacek |
| Organization name |
University of California San Francisco
|
| Street address |
1550 4th St. RH546 MC2922
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE254155 |
Nutrient Abundance Signals the Changing of the Seasons by Phosphorylating PER2 |
|
| Relations |
| BioSample |
SAMN39601020 |
| SRA |
SRX23385302 |
