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Sample GSM2301000 Query DataSets for GSM2301000
Status Public on Sep 22, 2016
Title Liver_tissue_from_24h_fasting_mice_rep2
Sample type SRA
 
Source name Liver tissue from 24h fasting mice
Organism Mus musculus
Characteristics tissue: Liver
condition: 24h fasting
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 6
Liver tissue from 24h fasting 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 SAMN05725799
SRA SRX2097310

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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