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| Status |
Public on Jun 03, 2024 |
| Title |
Liver,DD0-2,WT |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
strain: C57BL/6
genotype: WT
time point: DD0
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| Extracted molecule |
total RNA |
| Extraction protocol |
We extracted total RNA from tissue samples using Trizol (Invitrogen). After separating the RNA, DNA, and protein layers with chloroform, we precipitated the RNA using a standard isopropanol/ethanol procedure. The resulting RNA pellet was washed, and then resuspended in RNase-free water.
We assessed the quantity and quality of the total RNA using the Qubit RNA HS Assay (Life Technologies) and RNA 6000 Nano Assay on a Bioanalyzer 2100 (Agilent). For RNA-seq library construction, we followed the Illumina TruSeq Total RNA stranded protocol.
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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 |
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore (parameter:--phred33 --length 50 --stringency 3 --paired)
Trimmed sequence reads were mapped to GrCM38/mm10 using HISAT2 (parameters- -t -p 8 --dta --rna-strandness RF)
Read count extraction and normalization were performed using Samtools (parameters view -b -q 60) and featureCounts(parameters -T 16 -p -s 2)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample
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| Submission date |
Mar 16, 2023 |
| Last update date |
Jun 03, 2024 |
| Contact name |
Renrui Chen |
| E-mail(s) |
renruichen.bio@gmail.com
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| Organization name |
Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences
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| Street address |
No. 320 Yueyang Road
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| City |
Shanghai |
| ZIP/Postal code |
20031 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (2) |
| GSE227557 |
Circadian-affected tissue specificity is linked to aging and longevity [Differential expression analysis of liver and kidney] |
| GSE240693 |
Circadian-affected tissue specificity is linked to aging and longevity |
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| Relations |
| BioSample |
SAMN33789163 |
| SRA |
SRX19696743 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7102678_DD0-L2-1.txt.gz |
110.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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