|
| Status |
Public on Sep 22, 2016 |
| Title |
Liver_tissue_from_ad_libitum_mice_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Liver tissue from ad libitum mice
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
condition: Ad libitum
strain: C57BL/6
|
| Treatment protocol |
Male C57BL/6 mice from the Jackson Laboratory were used for all experiments. Groups of co-housed mice were randomly assigned to experimental groups with age and weight matched between groups. Mice of around 20 weeks of age were either allowed free access to food or were subjected to a 24-hour fast before being euthanized for tissue harvest (sacrificed at 10am).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted by Trizol reagent (Invitrogen) according to the manufacturer's instructions. Total RNA Cleanup with Dnase Digestion was performed using the Qiagen Rneasy Protocol.
The libraries were prepared from 1 ug of total RNA using the TruSeq® Stranded Total RNA Sample Preparation kit following manufacturer’s protocol (Illumina). Libraries were validated by Illumina miseq as recommended by the manufacturer.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Sample 2
Liver tissue from ad libitum mice, biological replicate 2
|
| Data processing |
Illumina bcl2fastq v2.17 software was used for basecalling.
The raw reads were mapped to the NONCODE 2016 mouse database using BWA (bwa aln; bwa sampe with the default parameters).
Proper-paired reads were then counted on each noncoding transcript to calculate the RPKM by normalizing the read count on each transcript with transcript length and total library size. Transcripts with RPKM >= 0 in at least one sample were retained.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file include NONCODE transcript IDs, annotations, raw reads, and RPKM values for all 8 Samples.
|
| |
|
| Submission date |
Sep 01, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Haiming Cao |
| E-mail(s) |
haiming.cao@nih.gov
|
| Phone |
3014029032
|
| Organization name |
NIH
|
| Department |
NHLBI
|
| Lab |
Laboratory of Obesity and Metabolic Diseases
|
| Street address |
9000 Rockville Pike
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE86371 |
RNA-Seq analyses of liver samples in mice fed ad libitum or subject to a 24 hr fast |
|
| Relations |
| BioSample |
SAMN05725797 |
| SRA |
SRX2097306 |
