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Status |
Public on Dec 31, 2019 |
Title |
W4_Lep1 |
Sample type |
SRA |
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Source name |
liver
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Organism |
Rattus norvegicus |
Characteristics |
tissue: liver
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted from snap-frozen liver samples using TRIzol (Life Technologies) according to the manufacturer’s instructions. RNA purity was checked using the Nano Photometer spectrophotometer (IMPLEN). RNA concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer (Life Technologies). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies). the libraries were sequenced on an Illumina Hiseq X platform and 150 bp paired-end reads were generated sequencing libraries were generated using the rRNA- depleted RNA by NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA)
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
HiSeq X Ten |
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Data processing |
Illumina Casava1.8 software used for basecalling. Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to rn6 or Macaca5 reference genome using hisat2 v2.1.0 with default parameters. Gene expression for each sample was quantified using featureCounts(v 1.6.1) and DEseq2(v 1.2.0). Genome_build: rn6;Macaca_fascicularis_5.0 Supplementary_files_format_and_content: rat_all_normat.csv: abundance measurements(DESeq2, log2-transformed) Supplementary_files_format_and_content: geneCounts_featureCounts_macaca.tab: abundance measurements(raw counts)
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Submission date |
Dec 18, 2018 |
Last update date |
Dec 31, 2019 |
Contact name |
Gran Young |
Organization name |
Tongji University
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Street address |
1239th, Siping Road, Yangpu district
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City |
Shanghai |
State/province |
--- Select a state --- |
ZIP/Postal code |
200082 |
Country |
China |
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Platform ID |
GPL24688 |
Series (1) |
GSE124002 |
Leptin deficiency leads to a unique natural history of NASH in rats |
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Relations |
BioSample |
SAMN10606739 |
SRA |
SRX5146492 |
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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