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| Status |
Public on Nov 01, 2020 |
| Title |
FCCL18 |
| Sample type |
SRA |
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| Source name |
total RNA isolated from mouse liver using the Trizol extraction technique and suspended in water
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| Organism |
Mus musculus |
| Characteristics |
sample id: Sample_3203
group id: HFD_O3
lineage: n-3PUFA
diet: HFD
tissue: Liver
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA were isolated using the Trizol reagent and washing steps with Isopropanol/Ethanol procedure before solubilization in sterile water
Small RNA-Seq librairies were generated from 800 ng of total RNA (or from --- ng of purified small RNA fraction) using TruSeq Small RNA Library Prep Kit (Illumina, San Diego, CA), according to manufacturer's instructions. The protocol takes advantage of the natural structure common to most microRNA molecules that have a 3' hydroxyl group resulting from enzymatic cleavage by Dicer or other RNA processing enzymes. Briefly, in the first step, RNA adapters were sequentially ligated to each end of the RNA, first the 3' RNA adapter that is specifically modified to target microRNAs and other small RNAs, then the 5' RNA adapter. Small RNA ligated with 3' and 5' adapters were reverse transcribed and PCR amplified (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 15 sec at 72oC] x 13 cycles; 10 min at 72oC) to create cDNA constructs. Amplified cDNA constructs of 140 to 160 nt were selectively isolated by acrylamide gel purification followed by ethanol precipitation. The final cDNA libraries were checked for quality and quantified using capillary electrophoresis.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Genome_build: mm10
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| Submission date |
Mar 05, 2020 |
| Last update date |
Nov 01, 2020 |
| Contact name |
frederic capel |
| E-mail(s) |
frederic.capel@inrae.fr
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| Phone |
33473178267
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| Organization name |
INRA
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| Department |
alimentation humaine
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| Lab |
ASMS
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| Street address |
28 place henri dunant
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| City |
clermont ferrand |
| ZIP/Postal code |
63001 |
| Country |
France |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE146445 |
SO-018 UNH: Influence of omega 3 supplementation over 3 generation of mice on the effect of metabolic stress in different organs |
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| Relations |
| BioSample |
SAMN14306676 |
| SRA |
SRX7856779 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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