|
| Status |
Public on Apr 25, 2019 |
| Title |
DR1ZT18 |
| Sample type |
SRA |
| |
|
| Source name |
Fed under arrhythmic feeding paradigm (did not adapt fully); sacrificed at ZT18
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
genotype: Wild-type
Sex: male
tissue: Liver
|
| Growth protocol |
Male C57BL/6J mice from Charles River Laboratories (starting age 43-49 days) were housed in a 12 hour light:12 hour dark facility with ad libitum access to water and variable access to food
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol reagent and purified with an acid phenol-chloroform extraction
3' mRNA libraries were prepared following manufacturer instructions for Lexogen's QuantSeq 3' mRNA-Seq Kit. 2μg input total RNA was used
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RAW_Table.txt
TPM_Table.txt
|
| Data processing |
Libraries were sequenced on an Illumina NextSeq. Base calling and demultiplexing were performed with the accompanying software
Sequenced reads were trimmed to remove the first 12nt, trailing and embedded polyA sequences, poor quality bases at the 3' end, and removed if under 36nt
Trimmed reads were aligned to mm10 transcriptome using STAR v2.4.2a with options "--outSAMstrandField intronMotif --quantMode GeneCounts --outFilterIntronMotifs RemoveNoncanonical"
Read counts were quantified to raw values with the R package GenomicRanges and normalized to 1 million transcripts per library (TPM)
Genes with under 1 TPM in 36 or more of the 72 libraries were removed from final consideration
Genome_build: mm10, GRCm38.p5
Supplementary_files_format_and_content: Tab-delimited text files with RAW (unnormalized or filtered) or TPM values for each gene and sample
|
| |
|
| Submission date |
Aug 23, 2018 |
| Last update date |
Apr 25, 2019 |
| Contact name |
Jerome Menet |
| E-mail(s) |
menetlab@gmail.com
|
| Organization name |
Texas A&M University
|
| Department |
Biology
|
| Lab |
Menet Laboratory
|
| Street address |
Texas A&M University Biology Department 3258 TAMU College Station, TX 77843
|
| City |
College Station |
| State/province |
Texas |
| ZIP/Postal code |
77843 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE118967 |
Rhythmic Food Intake Drives Rhythmic Gene Expression More Potently than the Hepatic Circadian Clock in Mice |
|
| Relations |
| BioSample |
SAMN09906276 |
| SRA |
SRX4603232 |
